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elax for a few days and watch how interactive programs are being composed**** TODO Get back to the real-world example and make it a complete Cabal project.**** TODO [[https://mmhaskell.com/testing/test-driven-development][Testing]]
**** Relax for a few days and watch how interactive programs are being composed**** Get back to the real-world example and make it a complete Cabal project.**** [[https://mmhaskell.com/testing/test-driven-development][Testing]]
***** TODO Anki****** TODO Grammaire**** TODO Leçon 7***** TODO Lire***** TODO Anki****** TODO Grammaire
***** KILL AnkiCLOSED: [2023-07-07 Fri 18:44]****** KILL GrammaireCLOSED: [2023-07-07 Fri 18:44]**** KILL Leçon 7CLOSED: [2023-07-07 Fri 18:44]***** KILL LireCLOSED: [2023-07-07 Fri 18:44]***** KILL AnkiCLOSED: [2023-07-07 Fri 18:44]****** KILL GrammaireCLOSED: [2023-07-07 Fri 18:44]
***** TODO Rajouter une colonne balance allélique****** STRT Ancien panel****** STRT Nouveau panel****** TODO Dijon***** HOLD Version executable pour paul
***** KILL Rajouter une colonne balance alléliqueCLOSED: [2023-07-07 Fri 18:47]****** KILL Ancien panelCLOSED: [2023-07-07 Fri 18:44]****** KILL Nouveau panelCLOSED: [2023-07-07 Fri 18:44]****** KILL DijonCLOSED: [2023-07-07 Fri 18:44]***** KILL Version executable pour paulCLOSED: [2023-07-07 Fri 18:44]
***** WAIT PED1078***** WAIT PED1079***** WAIT PED1080***** WAIT PED1083***** WAIT PED1084***** TODO PED1085***** TODO PED1086***** TODO PED1087***** TODO PED1088***** TODO PED1089***** TODO PED1150***** TODO PED1151***** TODO PED1152***** TODO PED1153***** TODO PED1154***** TODO PED1155***** TODO PED1156***** TODO PED1157***** TODO PED1158***** TODO PED1159***** TODO PED1160***** TODO PED1161***** TODO PED1165***** TODO PED1166***** TODO PED1167***** TODO PED1168***** TODO PED1174***** TODO PED1190***** TODO PED1191***** TODO PED1192***** TODO PED1193***** TODO PED1194***** TODO PED1227***** TODO PED1228***** TODO PED1273***** TODO PED1274***** TODO PED1275***** TODO PED1276***** TODO PED1277***** TODO PED1278***** TODO PED1344***** TODO PED1346***** TODO PED1347***** TODO PED1348***** TODO PED1351***** TODO PED1352***** TODO PED1402***** TODO PED1404***** TODO PED1405***** TODO PED1406***** TODO PED1407***** TODO PED1408***** TODO PED1409***** TODO PED1410***** TODO PED1411***** TODO PED1412***** TODO PED1413***** TODO PED1425***** TODO PED1429***** TODO PED1451***** TODO PED1494***** TODO PED1495***** TODO PED1496***** TODO PED1497***** TODO PED1498***** TODO PED1499***** TODO PED1500***** TODO PED1501***** TODO PED1502***** TODO PED1503***** TODO PED1523***** TODO PED1524***** TODO PED1570***** TODO PED1582***** TODO PED1583***** TODO PED1584***** TODO PED1585***** TODO PED1586***** TODO PED1587***** TODO PED1588***** TODO PED1589***** TODO PED1590***** TODO PED1591***** TODO PED1592***** TODO PED1593***** TODO PED1594***** TODO PED1595***** TODO PED1609***** TODO PED1610***** TODO PED1622***** TODO PED1623***** TODO PED1633
***** KILL PED1078CLOSED: [2023-07-07 Fri 18:44]***** KILL PED1079CLOSED: [2023-07-07 Fri 18:44]***** KILL PED1080CLOSED: [2023-07-07 Fri 18:44]***** KILL PED1083CLOSED: [2023-07-07 Fri 18:44]***** KILL PED1084CLOSED: [2023-07-07 Fri 18:44]***** KILL PED1085***** KILL PED1086***** KILL PED1087***** KILL PED1088***** KILL PED1089***** KILL PED1150***** KILL PED1151***** KILL PED1152***** KILL PED1153***** KILL PED1154***** KILL PED1155***** KILL PED1156***** KILL PED1157***** KILL PED1158***** KILL PED1159***** KILL PED1160***** KILL PED1161***** KILL PED1165***** KILL PED1166***** KILL PED1167***** KILL PED1168***** KILL PED1174***** KILL PED1190***** KILL PED1191***** KILL PED1192***** KILL PED1193***** KILL PED1194***** KILL PED1227***** KILL PED1228***** KILL PED1273***** KILL PED1274***** KILL PED1275***** KILL PED1276***** KILL PED1277***** KILL PED1278***** KILL PED1344***** KILL PED1346***** KILL PED1347***** KILL PED1348***** KILL PED1351***** KILL PED1352***** KILL PED1402***** KILL PED1404***** KILL PED1405***** KILL PED1406***** KILL PED1407***** KILL PED1408***** KILL PED1409***** KILL PED1410***** KILL PED1411***** KILL PED1412***** KILL PED1413***** KILL PED1425***** KILL PED1429***** KILL PED1451***** KILL PED1494***** KILL PED1495***** KILL PED1496***** KILL PED1497***** KILL PED1498***** KILL PED1499***** KILL PED1500***** KILL PED1501***** KILL PED1502***** KILL PED1503***** KILL PED1523***** KILL PED1524***** KILL PED1570***** KILL PED1582***** KILL PED1583***** KILL PED1584***** KILL PED1585***** KILL PED1586***** KILL PED1587***** KILL PED1588***** KILL PED1589***** KILL PED1590***** KILL PED1591***** KILL PED1592***** KILL PED1593***** KILL PED1594***** KILL PED1595***** KILL PED1609***** KILL PED1610***** KILL PED1622***** KILL PED1623***** KILL PED1633
***** TODO PED1635***** TODO PED1638***** TODO PED1679***** TODO PED1680***** TODO PED1681***** TODO PED1683***** TODO PED1685***** TODO PED1687***** TODO PED1815***** TODO PED1816***** TODO PED1881***** TODO PED1882***** TODO PED1883***** TODO PED1884***** TODO PED1885***** TODO PED1886***** TODO PED1887***** TODO PED1888***** TODO PED1901***** TODO PED1915***** TODO PED1916***** TODO PED1917***** TODO PED1931***** TODO PED1933***** TODO PED1934***** TODO PED1935***** TODO PED1947***** TODO PED1949***** TODO PED1950***** TODO PED1951***** TODO PED1953***** TODO PED1954***** TODO PED1955***** TODO PED1956***** TODO PED1957***** TODO PED1959***** TODO PED1962***** TODO PED1963***** TODO PED1965***** TODO PED1969***** TODO PED1970***** TODO PED1971***** TODO PED1972***** TODO PED1974***** TODO PED1975***** TODO PED1976***** TODO PED1977***** TODO PED1978***** TODO PED1979***** TODO PED1981***** TODO PED1982***** TODO PED1983***** TODO PED1984***** TODO PED1985***** TODO PED1986***** TODO PED1987***** TODO PED1988***** TODO PED1989***** TODO PED1990***** TODO PED1991***** TODO PED1992***** TODO PED1993***** TODO PED1996***** TODO PED2015***** TODO PED2016***** TODO PED2017***** TODO PED2018***** TODO PED2019***** TODO PED2050***** TODO PED2052***** TODO PED2068***** TODO PED2069***** TODO PED2070***** TODO PED2071***** TODO PED2072***** TODO PED2073***** TODO PED2074***** TODO PED2075***** TODO PED2076***** TODO PED2082***** TODO PED2086***** TODO PED2094***** TODO PED2097***** TODO PED2098***** TODO PED2099***** TODO PED2105***** TODO PED2111***** TODO PED2114***** TODO PED2128***** TODO PED2129***** TODO PED2134***** TODO PED2140***** TODO PED2141***** TODO PED2147***** TODO PED2153***** TODO PED2154***** TODO PED2155***** TODO PED2156***** TODO PED2157***** TODO PED2172***** TODO PED2173***** TODO PED2178***** TODO PED2179***** TODO PED2184***** TODO PED2191***** TODO PED2195***** TODO PED2200***** TODO PED2201***** TODO PED2202***** TODO PED2203***** TODO PED2204***** TODO PED2205***** TODO PED2212***** TODO PED2216***** TODO PED2217***** TODO PED2219***** TODO PED2220***** TODO PED2222***** TODO PED2227***** TODO PED2252***** TODO PED2253***** TODO PED2254***** TODO PED2262***** TODO PED2265***** TODO PED2270***** TODO PED2281***** TODO PED2282***** TODO PED2286***** TODO PED2301***** TODO PED2304***** TODO PED2306***** TODO PED2307***** TODO PED2308***** TODO PED2309***** TODO PED2310***** TODO PED2311***** TODO PED2312***** TODO PED2313***** TODO PED2317***** TODO PED2323***** TODO PED2325***** TODO PED2333***** TODO PED2338***** TODO PED2339***** TODO PED2341***** TODO PED2345***** TODO PED2346***** TODO PED2350***** TODO PED2353***** TODO PED2354***** TODO PED2355***** TODO PED2356***** TODO PED2357***** TODO PED2360***** TODO PED2363***** TODO PED2364***** TODO PED2366***** TODO PED2368***** TODO PED2369***** TODO PED2371***** TODO PED2376***** TODO PED2379***** TODO PED2380***** TODO PED2381***** TODO PED2392***** TODO PED2394***** TODO PED2396***** TODO PED2397***** TODO PED2398***** TODO PED2402***** TODO PED2405***** TODO PED2411***** TODO PED2412***** TODO PED2415***** TODO PED2417***** TODO PED2418***** TODO PED2421***** TODO PED2424***** TODO PED2428***** TODO PED2430***** TODO PED2441***** TODO PED2442***** TODO PED2476***** TODO PED2479***** TODO PED2480***** TODO PED2485***** TODO PED2486***** TODO PED2488***** TODO PED2492***** TODO PED2493***** TODO PED2494***** TODO PED2498***** TODO PED2500***** TODO PED2508***** TODO PED2513***** TODO PED2553***** TODO PED2558***** TODO PED2565***** TODO PED2569***** TODO PED2578***** TODO PED2579***** TODO PED2580***** TODO PED2583***** TODO PED2586***** TODO PED2587***** TODO PED2588***** TODO PED2593***** TODO PED2594***** TODO PED2597***** TODO PED2598***** TODO PED2605***** TODO PED2606***** TODO PED2613***** TODO PED2615***** TODO PED2616***** TODO PED2619***** TODO PED2621***** TODO PED2623***** TODO PED2627***** TODO PED2629***** TODO PED2634***** TODO PED2636***** TODO PED2637***** TODO PED2640***** TODO PED2643***** TODO PED2656***** TODO PED2659***** TODO PED2660***** TODO PED2661***** TODO PED2662***** TODO PED2674***** TODO PED2678***** TODO PED2679***** TODO PED2682***** TODO PED2687***** TODO PED2689***** TODO PED2690***** TODO PED2694***** TODO PED2697***** TODO PED2699***** TODO PED2702***** TODO PED2705***** TODO PED2714***** TODO PED2715***** TODO PED2716***** TODO PED2718***** TODO PED2722***** TODO PED2725***** TODO PED2726***** TODO PED2727***** TODO PED2728***** TODO PED2737***** TODO PED2738***** TODO PED2739***** TODO PED2741***** TODO PED2742***** TODO PED2743***** TODO PED2744***** TODO PED2747***** TODO PED2756***** TODO PED2758***** TODO PED2760***** TODO PED2761***** TODO PED2765***** TODO PED2766***** TODO PED2767***** TODO PED2769***** TODO PED2771***** TODO PED2774***** TODO PED2780***** TODO PED2781***** TODO PED2782***** TODO PED2787***** TODO PED2792***** TODO PED2793***** TODO PED2799***** TODO PED2800***** TODO PED2801***** TODO PED2802***** TODO PED2820***** TODO PED2824***** TODO PED2825***** TODO PED2828***** TODO PED2832***** TODO PED2836***** TODO PED2837***** TODO PED2838***** TODO PED2844***** TODO PED2846***** TODO PED2848***** TODO PED2850***** TODO PED2852***** TODO PED2862***** TODO PED2866***** TODO PED2872***** TODO PED2875***** TODO PED2877***** TODO PED2878***** TODO PED2882***** TODO PED2884***** TODO PED2885***** TODO PED2899***** TODO PED2904***** TODO PED2905***** TODO PED2909***** TODO PED2919***** TODO PED2920***** TODO PED2925***** TODO PED3004***** TODO PED3018***** TODO PED3020***** TODO PED3025***** TODO PED3027***** TODO PED3029***** TODO PED3030***** TODO PED3032***** TODO PED3033***** TODO PED3035***** TODO PED3037***** TODO PED3043***** TODO PED3046***** TODO PED3048***** TODO PED3075***** TODO PED3076***** TODO PED3077***** TODO PED3078***** TODO PED3152***** TODO PED3155***** TODO PED3161***** TODO PED3163***** TODO PED3165***** TODO PED3170***** TODO PED3173***** TODO PED3174***** TODO PED3176***** TODO PED3179***** TODO PED3248***** TODO PED3256***** TODO PED3265***** TODO PED3294***** TODO PED3302***** TODO PED3304***** TODO PED3324***** TODO PED3331***** TODO PED3337***** TODO PED3342***** TODO PED3344***** TODO PED3348***** TODO PED3351***** TODO PED3366***** TODO PED3370***** TODO PED3385***** TODO PED3396***** TODO PED3397***** TODO PED3410***** TODO PED3416***** TODO PED3417***** TODO PED3426***** TODO PED3456***** TODO PED3458***** TODO PED3464***** TODO PED3467***** TODO PED3472***** TODO PED3475***** TODO PED3477***** TODO PED3480***** TODO PED3485***** TODO PED3496***** TODO PED3524***** TODO PED3530***** TODO PED3534***** TODO PED3550***** TODO PED3563***** TODO PED3569***** TODO PED3576***** TODO PED3577***** TODO PED3578***** TODO PED3645***** TODO PED3649***** TODO PED3655***** TODO PED3661***** TODO PED3664***** TODO PED3670***** TODO PED3680***** TODO PED3681***** TODO PED3683***** TODO PED3685***** TODO PED3689***** TODO PED3692***** TODO PED3708***** TODO PED3714***** TODO PED3723***** TODO PED3725***** TODO PED3727***** TODO PED3730***** TODO PED3749***** TODO PED3751***** TODO PED3752***** TODO PED3753***** TODO PED3760***** TODO PED3765***** TODO PED3766***** TODO PED3767***** TODO PED3771***** TODO PED3781***** TODO PED3782***** TODO PED3791***** TODO PED3792***** TODO PED3796***** TODO PED3798***** TODO PED3823***** TODO PED3829***** TODO PED3839***** TODO PED3840***** TODO PED3848***** TODO PED3849***** TODO PED3862***** TODO PED3881***** TODO PED3883***** TODO PED3886***** TODO PED3894***** TODO PED3895***** TODO PED3901***** TODO PED3904***** TODO PED3915***** TODO PED3919***** TODO PED3927***** TODO PED3928***** TODO PED3930***** TODO PED3937***** TODO PED3939***** TODO PED3940***** TODO PED3943***** TODO PED3951***** TODO PED3955***** TODO PED3956***** TODO PED3959***** TODO PED3960***** TODO PED3961***** TODO PED3970***** TODO PED3979***** TODO PED3996***** TODO PED3999***** TODO PED4001***** TODO PED4009***** TODO PED4037***** TODO PED4040***** TODO PED4044***** TODO PED4046***** TODO PED4048***** TODO PED4051***** TODO PED4065***** TODO PED4068***** TODO PED4069***** TODO PED4079***** TODO PED4080***** TODO PED4100***** TODO PED4104***** TODO PED4110***** TODO PED4111***** TODO PED4113***** TODO PED4114***** TODO PED4118***** TODO PED4128***** TODO PED4131***** TODO PED4133***** TODO PED4135***** TODO PED4136***** TODO PED4142***** TODO PED4161***** TODO PED4163***** TODO PED4164***** TODO PED4165***** TODO PED4199***** TODO PED4203***** TODO PED4204***** TODO PED4208***** TODO PED4213***** TODO PED4214***** TODO PED4223***** TODO PED4226***** TODO PED4227***** TODO PED4234***** TODO PED4235***** TODO PED4236***** TODO PED4237***** TODO PED4238***** TODO PED4239***** TODO PED4240***** TODO PED4241***** TODO PED4248***** TODO PED4256***** TODO PED4260***** TODO PED4263***** TODO PED4266***** TODO PED4275***** TODO PED4284***** TODO PED4287***** TODO PED4302***** TODO PED4309***** TODO PED4321***** TODO PED4326***** TODO PED4332***** TODO PED4336***** TODO PED4338***** TODO PED4347***** TODO PED4363***** TODO PED4376***** TODO PED4377***** TODO PED4383***** TODO PED4384***** TODO PED4387***** TODO PED4396***** TODO PED4416***** TODO PED4421***** TODO PED4433***** TODO PED4439***** TODO PED4440***** TODO PED4443***** TODO PED4445***** TODO PED4447***** TODO PED4452***** TODO PED4457***** TODO PED4461***** TODO PED4464***** TODO PED4470***** TODO PED4479***** TODO PED4485***** TODO PED4500***** TODO PED4503***** TODO PED4507***** TODO PED4527***** TODO PED4528***** TODO PED4529***** TODO PED4530***** TODO PED4535***** TODO PED4538***** TODO PED4540***** TODO PED4558***** TODO PED4565***** TODO PED4581***** TODO PED4590***** TODO PED4594***** TODO PED4597***** TODO PED4599***** TODO PED4601***** TODO PED4622***** TODO PED4624***** TODO PED4629***** TODO PED4638***** TODO PED4642***** TODO PED4648***** TODO PED4670***** TODO PED4674***** TODO PED4677***** TODO PED4679***** TODO PED4683***** TODO PED4684***** TODO PED4685***** TODO PED4686***** TODO PED4695***** TODO PED4699***** TODO PED4711***** TODO PED4713***** TODO PED4719***** TODO PED4720***** TODO PED4726***** TODO PED4729***** TODO PED4744***** TODO PED4760***** TODO PED4764***** TODO PED4768***** TODO PED4777***** TODO PED4788***** TODO PED4789***** TODO PED4794***** TODO PED4799***** TODO PED4800***** TODO PED4801***** TODO PED4818***** TODO PED4820***** TODO PED4848***** TODO PED4849***** TODO PED4850***** TODO PED4872***** TODO PED4877***** TODO PED4889***** TODO PED4895***** TODO PED4905***** TODO PED4914***** TODO PED4917***** TODO PED4920***** TODO PED4921***** TODO PED4928***** TODO PED4940***** TODO PED4941***** TODO PED4942***** TODO PED4943***** TODO PED4944***** TODO PED4955***** TODO PED4959***** TODO PED4965***** TODO PED4967***** TODO PED4968***** TODO PED4975***** TODO PED4983***** TODO PED4984***** TODO PED4989***** TODO PED4997***** TODO PED5000***** TODO PED5005***** TODO PED5006***** TODO PED5007***** TODO PED5013***** TODO PED5014***** TODO PED5031***** TODO PED5042***** TODO PED5045***** TODO PED5053***** TODO PED5058***** TODO PED5059***** TODO PED5066***** TODO PED5076***** TODO PED5087***** TODO PED5099***** TODO PED5103***** TODO PED5104***** TODO PED5113***** TODO PED5121***** TODO PED5125***** TODO PED5144***** TODO PED5145***** TODO PED5146***** TODO PED5148***** TODO PED5152***** TODO PED5160***** TODO PED5162***** TODO PED5163***** TODO PED5164***** TODO PED5177***** TODO PED5182***** TODO PED5183***** TODO PED5184***** TODO PED5185***** TODO PED5189***** TODO PED5197***** TODO PED5201***** TODO PED5202***** TODO PED5206***** TODO PED5211***** TODO PED5214***** TODO PED5221***** TODO PED5234***** TODO PED5242***** TODO PED5258***** TODO PED5263***** TODO PED5264***** TODO PED5292***** TODO PED5293***** TODO PED5312***** TODO PED5319***** TODO PED5327***** TODO PED5328***** TODO PED5329***** TODO PED5330***** TODO PED5331***** TODO PED5332***** TODO PED5333***** TODO PED5337***** TODO PED5345***** TODO PED5351***** TODO PED5352***** TODO PED5353***** TODO PED5372***** TODO PED5380***** TODO PED5384***** TODO PED5389***** TODO PED5399***** TODO PED5401***** TODO PED5402***** TODO PED5403***** TODO PED5409***** TODO PED5415***** TODO PED5419***** TODO PED5427***** TODO PED5439***** TODO PED5440***** TODO PED5442***** TODO PED5452***** TODO PED5461***** TODO PED5465***** TODO PED5488***** TODO PED5489***** TODO PED5508***** TODO PED5511***** TODO PED5514***** TODO PED5515***** TODO PED5523***** TODO PED5524***** TODO PED5525***** TODO PED5543***** TODO PED5552***** TODO PED5553***** TODO PED5558***** TODO PED5571***** TODO PED5574***** TODO PED5576***** TODO PED5582***** TODO PED5584***** TODO PED5585***** TODO PED5586***** TODO PED5592***** TODO PED5593***** TODO PED5594***** TODO PED5599***** TODO PED5607***** TODO PED5608***** TODO PED5619***** TODO PED5620***** TODO PED5629***** TODO PED5639***** TODO PED5642***** TODO PED5653***** TODO PED5661***** TODO PED5662***** TODO PED5666***** TODO PED5669***** TODO PED5670***** TODO PED5672***** TODO PED5676***** TODO PED5684***** TODO PED5697***** TODO PED5700***** TODO PED5718***** TODO PED5724***** TODO PED5725***** TODO PED5726***** TODO PED5727***** TODO PED5730***** TODO PED5731***** TODO PED5737***** TODO PED5738***** TODO PED5743***** TODO PED5749***** TODO PED5760***** TODO PED5768***** TODO PED5769***** TODO PED5781***** TODO PED5796***** TODO PED5798***** TODO PED5807***** TODO PED5812***** TODO PED5815***** TODO PED5816***** TODO PED5827***** TODO PED5866***** TODO PED5867***** TODO PED5868***** TODO PED5870***** TODO PED5871***** TODO PED5873***** TODO PED5900***** TODO PED5901***** TODO PED5911***** TODO PED5926***** TODO PED5928***** TODO PED5930***** TODO PED6035***** TODO PED6048***** TODO PED6049***** TODO PED6056***** TODO PED6066***** TODO PED6079***** TODO PED6080***** TODO PED6087***** TODO PED6088***** TODO PED6100***** TODO PED6101***** TODO PED6107***** TODO PED6113***** TODO PED6114***** TODO PED6115***** TODO PED6116***** TODO PED6117***** TODO PED6118***** TODO PED6121***** TODO PED6135***** TODO PED6143***** TODO PED6144***** TODO PED6158***** TODO PED6174***** TODO PED6187***** TODO PED6189***** TODO PED6190***** TODO PED6196***** TODO PED6205***** TODO PED6206***** TODO PED6208***** TODO PED6213***** TODO PED6217***** TODO PED6220***** TODO PED6222***** TODO PED6223***** TODO PED6224***** TODO PED6233***** TODO PED6235***** TODO PED6241***** TODO PED6252***** TODO PED6256***** TODO PED6263***** TODO PED6275***** TODO PED6280***** TODO PED6347***** TODO PED6359***** TODO PED6369***** TODO PED6370***** TODO PED6385***** TODO PED6414***** TODO PED6430***** TODO PED6438***** TODO PED6450***** TODO PED6460***** TODO PED6467***** TODO PED6468***** TODO PED6474***** TODO PED6915***** TODO PED6918***** TODO PED6928***** TODO PED6931***** TODO PED6940***** TODO PED6941***** TODO PED6945***** TODO PED6956***** TODO PED6988***** TODO PED7001***** TODO PED7016***** TODO PED7041***** TODO PED7047***** TODO PED7051***** TODO PED7052***** TODO PED7053***** TODO PED7054***** TODO PED7057***** TODO PED7061***** TODO PED7067***** TODO PED7076***** TODO PED7086***** TODO PED7092***** TODO PED7101***** TODO PED7105***** TODO PED7121***** TODO PED7162***** TODO PED7163***** TODO PED7165***** TODO PED7167***** TODO PED7187***** TODO PED7197***** TODO PED7198***** TODO PED7201***** TODO PED7202***** TODO PED7207***** TODO PED7227***** TODO PED7228***** TODO PED7230***** TODO PED7252***** TODO PED7277***** TODO PED7281***** TODO PED7289***** TODO PED7293***** TODO PED7321***** TODO PED7329***** TODO PED7331***** TODO PED7341***** TODO PED7343***** TODO PED7347***** TODO PED7391***** TODO PED7393***** TODO PED7394***** TODO PED7421***** TODO PED7422***** TODO PED7432***** TODO PED7435***** TODO PED7436***** TODO PED7437***** TODO PED7447***** TODO PED7471***** TODO PED7472***** TODO PED7507***** TODO PED7508***** TODO PED7509***** TODO PED7534***** TODO PED7548***** TODO PED7557***** TODO PED7568***** TODO PED7575***** TODO PED7581***** TODO PED7582***** TODO PED7589***** TODO PED7601***** TODO PED7612***** TODO PED7613***** TODO PED7637***** TODO PED7638***** TODO PED7643***** TODO PED7647***** TODO PED7653***** TODO PED7665***** TODO PED7674***** TODO PED7718***** TODO PED7722***** TODO PED7732***** TODO PED7735***** TODO PED7740***** TODO PED7741***** TODO PED7745***** TODO PED7756***** TODO PED7761***** TODO PED7767***** TODO PED7769***** TODO PED7770***** TODO PED7773***** TODO PED7778***** TODO PED7791***** TODO PED7806***** TODO PED7807***** TODO PED7808***** TODO PED7817***** TODO PED7823***** TODO PED7827***** TODO PED7835***** TODO PED7846***** TODO PED7857***** TODO PED7875***** TODO PED7876***** TODO PED7885***** TODO PED7902***** TODO PED7905***** TODO PED7914***** TODO PED7937***** TODO PED7938***** TODO PED7942***** TODO PED7962***** TODO PED7963***** TODO PED7964***** TODO PED7965***** TODO PED7966***** TODO PED7967***** TODO PED7997***** TODO PED8002***** TODO PED8003***** TODO PED8013***** TODO PED8014***** TODO PED8015***** TODO PED8021***** TODO PED8035***** TODO PED8050***** TODO PED8052***** TODO PED8056***** TODO PED8074***** TODO PED8098***** TODO PED8099***** TODO PED8105***** TODO PED8114***** TODO PED8121***** TODO PED8130***** TODO PED8149***** TODO PED8151***** TODO PED8155***** TODO PED8172***** TODO PED8195***** TODO PED8203***** TODO PED8210***** TODO PED8214***** TODO PED8267***** TODO PED8294***** TODO PED8295***** TODO PED8315***** TODO PED8321***** TODO PED8323***** TODO PED8334***** TODO PED8366***** TODO PED8368***** TODO PED8375***** TODO PED8376***** TODO PED8379***** TODO PED8429***** TODO PED8437***** TODO PED8461***** TODO PED8494***** TODO PED8501***** TODO PED8511***** TODO PED8517***** TODO PED8525***** TODO PED8540***** TODO PED8541***** TODO PED8558***** TODO PED8580***** TODO PED8582***** TODO PED8593***** TODO PED8595***** TODO PED8603***** TODO PED8608***** TODO PED8614***** TODO PED8615***** TODO PED8617***** TODO PED8618***** TODO PED8622***** TODO PED8624***** TODO PED8631***** TODO PED8634***** TODO PED8635***** TODO PED8636***** TODO PED8637***** TODO PED8638***** TODO PED8641***** TODO PED8654***** TODO PED8660***** TODO PED8661***** TODO PED8663***** TODO PED8670***** TODO PED8680***** TODO PED8685***** TODO PED8687***** TODO PED8690***** TODO PED8693***** TODO PED8709***** TODO PED8722***** TODO PED8790***** TODO PED8801***** TODO PED8807***** TODO PED8810***** TODO PED8816***** TODO PED8818***** TODO PED8832***** TODO PED8852***** TODO PED8866***** TODO PED8869***** TODO PED8870***** TODO PED8878***** TODO PED8894***** TODO PED8917***** TODO PED8937***** TODO PED8947***** TODO PED8951***** TODO PED8961***** TODO PED9013***** TODO PED9024***** TODO PED9051***** TODO PED9057***** TODO PED9074***** TODO PED9083***** TODO PED9088***** TODO PED9095***** TODO PED9131***** TODO PED9152***** TODO PED9181***** TODO PED9200***** TODO PED9202***** TODO PED9252***** TODO PED9270***** TODO PED9271***** TODO PED9281***** TODO PED9282***** TODO PED9285***** TODO PED9286***** TODO PED9287***** TODO PED9345***** TODO PED9367***** TODO PED9368***** TODO PED9405***** TODO PED9430***** TODO PED9440***** TODO PED9445***** TODO PED9456***** TODO PED9458***** TODO PED9528***** TODO PED9559***** TODO PED9740
***** KILL PED1635***** KILL PED1638***** KILL PED1679***** KILL PED1680***** KILL PED1681***** KILL PED1683***** KILL PED1685***** KILL PED1687***** KILL PED1815***** KILL PED1816***** KILL PED1881***** KILL PED1882***** KILL PED1883***** KILL PED1884***** KILL PED1885***** KILL PED1886***** KILL PED1887***** KILL PED1888***** KILL PED1901***** KILL PED1915***** KILL PED1916***** KILL PED1917***** KILL PED1931***** KILL PED1933***** KILL PED1934***** KILL PED1935***** KILL PED1947***** KILL PED1949***** KILL PED1950***** KILL PED1951***** KILL PED1953***** KILL PED1954***** KILL PED1955***** KILL PED1956***** KILL PED1957***** KILL PED1959***** KILL PED1962***** KILL PED1963***** KILL PED1965***** KILL PED1969***** KILL PED1970***** KILL PED1971***** KILL PED1972***** KILL PED1974***** KILL PED1975***** KILL PED1976***** KILL PED1977***** KILL PED1978***** KILL PED1979***** KILL PED1981***** KILL PED1982***** KILL PED1983***** KILL PED1984***** KILL PED1985***** KILL PED1986***** KILL PED1987***** KILL PED1988***** KILL PED1989***** KILL PED1990***** KILL PED1991***** KILL PED1992***** KILL PED1993***** KILL PED1996***** KILL PED2015***** KILL PED2016***** KILL PED2017***** KILL PED2018***** KILL PED2019***** KILL PED2050***** KILL PED2052***** KILL PED2068***** KILL PED2069***** KILL PED2070***** KILL PED2071***** KILL PED2072***** KILL PED2073***** KILL PED2074***** KILL PED2075***** KILL PED2076***** KILL PED2082***** KILL PED2086***** KILL PED2094***** KILL PED2097***** KILL PED2098***** KILL PED2099***** KILL PED2105***** KILL PED2111***** KILL PED2114***** KILL PED2128***** KILL PED2129***** KILL PED2134***** KILL PED2140***** KILL PED2141***** KILL PED2147***** KILL PED2153***** KILL PED2154***** KILL PED2155***** KILL PED2156***** KILL PED2157***** KILL PED2172***** KILL PED2173***** KILL PED2178***** KILL PED2179***** KILL PED2184***** KILL PED2191***** KILL PED2195***** KILL PED2200***** KILL PED2201***** KILL PED2202***** KILL PED2203***** KILL PED2204***** KILL PED2205***** KILL PED2212***** KILL PED2216***** KILL PED2217***** KILL PED2219***** KILL PED2220***** KILL PED2222***** KILL PED2227***** KILL PED2252***** KILL PED2253***** KILL PED2254***** KILL PED2262***** KILL PED2265***** KILL PED2270***** KILL PED2281***** KILL PED2282***** KILL PED2286***** KILL PED2301***** KILL PED2304***** KILL PED2306***** KILL PED2307***** KILL PED2308***** KILL PED2309***** KILL PED2310***** KILL PED2311***** KILL PED2312***** KILL PED2313***** KILL PED2317***** KILL PED2323***** KILL PED2325***** KILL PED2333***** KILL PED2338***** KILL PED2339***** KILL PED2341***** KILL PED2345***** KILL PED2346***** KILL PED2350***** KILL PED2353***** KILL PED2354***** KILL PED2355***** KILL PED2356***** KILL PED2357***** KILL PED2360***** KILL PED2363***** KILL PED2364***** KILL PED2366***** KILL PED2368***** KILL PED2369***** KILL PED2371***** KILL PED2376***** KILL PED2379***** KILL PED2380***** KILL PED2381***** KILL PED2392***** KILL PED2394***** KILL PED2396***** KILL PED2397***** KILL PED2398***** KILL PED2402***** KILL PED2405***** KILL PED2411***** KILL PED2412***** KILL PED2415***** KILL PED2417***** KILL PED2418***** KILL PED2421***** KILL PED2424***** KILL PED2428***** KILL PED2430***** KILL PED2441***** KILL PED2442***** KILL PED2476***** KILL PED2479***** KILL PED2480***** KILL PED2485***** KILL PED2486***** KILL PED2488***** KILL PED2492***** KILL PED2493***** KILL PED2494***** KILL PED2498***** KILL PED2500***** KILL PED2508***** KILL PED2513***** KILL PED2553***** KILL PED2558***** KILL PED2565***** KILL PED2569***** KILL PED2578***** KILL PED2579***** KILL PED2580***** KILL PED2583***** KILL PED2586***** KILL PED2587***** KILL PED2588***** KILL PED2593***** KILL PED2594***** KILL PED2597***** KILL PED2598***** KILL PED2605***** KILL PED2606***** KILL PED2613***** KILL PED2615***** KILL PED2616***** KILL PED2619***** KILL PED2621***** KILL PED2623***** KILL PED2627***** KILL PED2629***** KILL PED2634***** KILL PED2636***** KILL PED2637***** KILL PED2640***** KILL PED2643***** KILL PED2656***** KILL PED2659***** KILL PED2660***** KILL PED2661***** KILL PED2662***** KILL PED2674***** KILL PED2678***** KILL PED2679***** KILL PED2682***** KILL PED2687***** KILL PED2689***** KILL PED2690***** KILL PED2694***** KILL PED2697***** KILL PED2699***** KILL PED2702***** KILL PED2705***** KILL PED2714***** KILL PED2715***** KILL PED2716***** KILL PED2718***** KILL PED2722***** KILL PED2725***** KILL PED2726***** KILL PED2727***** KILL PED2728***** KILL PED2737***** KILL PED2738***** KILL PED2739***** KILL PED2741***** KILL PED2742***** KILL PED2743***** KILL PED2744***** KILL PED2747***** KILL PED2756***** KILL PED2758***** KILL PED2760***** KILL PED2761***** KILL PED2765***** KILL PED2766***** KILL PED2767***** KILL PED2769***** KILL PED2771***** KILL PED2774***** KILL PED2780***** KILL PED2781***** KILL PED2782***** KILL PED2787***** KILL PED2792***** KILL PED2793***** KILL PED2799***** KILL PED2800***** KILL PED2801***** KILL PED2802***** KILL PED2820***** KILL PED2824***** KILL PED2825***** KILL PED2828***** KILL PED2832***** KILL PED2836***** KILL PED2837***** KILL PED2838***** KILL PED2844***** KILL PED2846***** KILL PED2848***** KILL PED2850***** KILL PED2852***** KILL PED2862***** KILL PED2866***** KILL PED2872***** KILL PED2875***** KILL PED2877***** KILL PED2878***** KILL PED2882***** KILL PED2884***** KILL PED2885***** KILL PED2899***** KILL PED2904***** KILL PED2905***** KILL PED2909***** KILL PED2919***** KILL PED2920***** KILL PED2925***** KILL PED3004***** KILL PED3018***** KILL PED3020***** KILL PED3025***** KILL PED3027***** KILL PED3029***** KILL PED3030***** KILL PED3032***** KILL PED3033***** KILL PED3035***** KILL PED3037***** KILL PED3043***** KILL PED3046***** KILL PED3048***** KILL PED3075***** KILL PED3076***** KILL PED3077***** KILL PED3078***** KILL PED3152***** KILL PED3155***** KILL PED3161***** KILL PED3163***** KILL PED3165***** KILL PED3170***** KILL PED3173***** KILL PED3174***** KILL PED3176***** KILL PED3179***** KILL PED3248***** KILL PED3256***** KILL PED3265***** KILL PED3294***** KILL PED3302***** KILL PED3304***** KILL PED3324***** KILL PED3331***** KILL PED3337***** KILL PED3342***** KILL PED3344***** KILL PED3348***** KILL PED3351***** KILL PED3366***** KILL PED3370***** KILL PED3385***** KILL PED3396***** KILL PED3397***** KILL PED3410***** KILL PED3416***** KILL PED3417***** KILL PED3426***** KILL PED3456***** KILL PED3458***** KILL PED3464***** KILL PED3467***** KILL PED3472***** KILL PED3475***** KILL PED3477***** KILL PED3480***** KILL PED3485***** KILL PED3496***** KILL PED3524***** KILL PED3530***** KILL PED3534***** KILL PED3550***** KILL PED3563***** KILL PED3569***** KILL PED3576***** KILL PED3577***** KILL PED3578***** KILL PED3645***** KILL PED3649***** KILL PED3655***** KILL PED3661***** KILL PED3664***** KILL PED3670***** KILL PED3680***** KILL PED3681***** KILL PED3683***** KILL PED3685***** KILL PED3689***** KILL PED3692***** KILL PED3708***** KILL PED3714***** KILL PED3723***** KILL PED3725***** KILL PED3727***** KILL PED3730***** KILL PED3749***** KILL PED3751***** KILL PED3752***** KILL PED3753***** KILL PED3760***** KILL PED3765***** KILL PED3766***** KILL PED3767***** KILL PED3771***** KILL PED3781***** KILL PED3782***** KILL PED3791***** KILL PED3792***** KILL PED3796***** KILL PED3798***** KILL PED3823***** KILL PED3829***** KILL PED3839***** KILL PED3840***** KILL PED3848***** KILL PED3849***** KILL PED3862***** KILL PED3881***** KILL PED3883***** KILL PED3886***** KILL PED3894***** KILL PED3895***** KILL PED3901***** KILL PED3904***** KILL PED3915***** KILL PED3919***** KILL PED3927***** KILL PED3928***** KILL PED3930***** KILL PED3937***** KILL PED3939***** KILL PED3940***** KILL PED3943***** KILL PED3951***** KILL PED3955***** KILL PED3956***** KILL PED3959***** KILL PED3960***** KILL PED3961***** KILL PED3970***** KILL PED3979***** KILL PED3996***** KILL PED3999***** KILL PED4001***** KILL PED4009***** KILL PED4037***** KILL PED4040***** KILL PED4044***** KILL PED4046***** KILL PED4048***** KILL PED4051***** KILL PED4065***** KILL PED4068***** KILL PED4069***** KILL PED4079***** KILL PED4080***** KILL PED4100***** KILL PED4104***** KILL PED4110***** KILL PED4111***** KILL PED4113***** KILL PED4114***** KILL PED4118***** KILL PED4128***** KILL PED4131***** KILL PED4133***** KILL PED4135***** KILL PED4136***** KILL PED4142***** KILL PED4161***** KILL PED4163***** KILL PED4164***** KILL PED4165***** KILL PED4199***** KILL PED4203***** KILL PED4204***** KILL PED4208***** KILL PED4213***** KILL PED4214***** KILL PED4223***** KILL PED4226***** KILL PED4227***** KILL PED4234***** KILL PED4235***** KILL PED4236***** KILL PED4237***** KILL PED4238***** KILL PED4239***** KILL PED4240***** KILL PED4241***** KILL PED4248***** KILL PED4256***** KILL PED4260***** KILL PED4263***** KILL PED4266***** KILL PED4275***** KILL PED4284***** KILL PED4287***** KILL PED4302***** KILL PED4309***** KILL PED4321***** KILL PED4326***** KILL PED4332***** KILL PED4336***** KILL PED4338***** KILL PED4347***** KILL PED4363***** KILL PED4376***** KILL PED4377***** KILL PED4383***** KILL PED4384***** KILL PED4387***** KILL PED4396***** KILL PED4416***** KILL PED4421***** KILL PED4433***** KILL PED4439***** KILL PED4440***** KILL PED4443***** KILL PED4445***** KILL PED4447***** KILL PED4452***** KILL PED4457***** KILL PED4461***** KILL PED4464***** KILL PED4470***** KILL PED4479***** KILL PED4485***** KILL PED4500***** KILL PED4503***** KILL PED4507***** KILL PED4527***** KILL PED4528***** KILL PED4529***** KILL PED4530***** KILL PED4535***** KILL PED4538***** KILL PED4540***** KILL PED4558***** KILL PED4565***** KILL PED4581***** KILL PED4590***** KILL PED4594***** KILL PED4597***** KILL PED4599***** KILL PED4601***** KILL PED4622***** KILL PED4624***** KILL PED4629***** KILL PED4638***** KILL PED4642***** KILL PED4648***** KILL PED4670***** KILL PED4674***** KILL PED4677***** KILL PED4679***** KILL PED4683***** KILL PED4684***** KILL PED4685***** KILL PED4686***** KILL PED4695***** KILL PED4699***** KILL PED4711***** KILL PED4713***** KILL PED4719***** KILL PED4720***** KILL PED4726***** KILL PED4729***** KILL PED4744***** KILL PED4760***** KILL PED4764***** KILL PED4768***** KILL PED4777***** KILL PED4788***** KILL PED4789***** KILL PED4794***** KILL PED4799***** KILL PED4800***** KILL PED4801***** KILL PED4818***** KILL PED4820***** KILL PED4848***** KILL PED4849***** KILL PED4850***** KILL PED4872***** KILL PED4877***** KILL PED4889***** KILL PED4895***** KILL PED4905***** KILL PED4914***** KILL PED4917***** KILL PED4920***** KILL PED4921***** KILL PED4928***** KILL PED4940***** KILL PED4941***** KILL PED4942***** KILL PED4943***** KILL PED4944***** KILL PED4955***** KILL PED4959***** KILL PED4965***** KILL PED4967***** KILL PED4968***** KILL PED4975***** KILL PED4983***** KILL PED4984***** KILL PED4989***** KILL PED4997***** KILL PED5000***** KILL PED5005***** KILL PED5006***** KILL PED5007***** KILL PED5013***** KILL PED5014***** KILL PED5031***** KILL PED5042***** KILL PED5045***** KILL PED5053***** KILL PED5058***** KILL PED5059***** KILL PED5066***** KILL PED5076***** KILL PED5087***** KILL PED5099***** KILL PED5103***** KILL PED5104***** KILL PED5113***** KILL PED5121***** KILL PED5125***** KILL PED5144***** KILL PED5145***** KILL PED5146***** KILL PED5148***** KILL PED5152***** KILL PED5160***** KILL PED5162***** KILL PED5163***** KILL PED5164***** KILL PED5177***** KILL PED5182***** KILL PED5183***** KILL PED5184***** KILL PED5185***** KILL PED5189***** KILL PED5197***** KILL PED5201***** KILL PED5202***** KILL PED5206***** KILL PED5211***** KILL PED5214***** KILL PED5221***** KILL PED5234***** KILL PED5242***** KILL PED5258***** KILL PED5263***** KILL PED5264***** KILL PED5292***** KILL PED5293***** KILL PED5312***** KILL PED5319***** KILL PED5327***** KILL PED5328***** KILL PED5329***** KILL PED5330***** KILL PED5331***** KILL PED5332***** KILL PED5333***** KILL PED5337***** KILL PED5345***** KILL PED5351***** KILL PED5352***** KILL PED5353***** KILL PED5372***** KILL PED5380***** KILL PED5384***** KILL PED5389***** KILL PED5399***** KILL PED5401***** KILL PED5402***** KILL PED5403***** KILL PED5409***** KILL PED5415***** KILL PED5419***** KILL PED5427***** KILL PED5439***** KILL PED5440***** KILL PED5442***** KILL PED5452***** KILL PED5461***** KILL PED5465***** KILL PED5488***** KILL PED5489***** KILL PED5508***** KILL PED5511***** KILL PED5514***** KILL PED5515***** KILL PED5523***** KILL PED5524***** KILL PED5525***** KILL PED5543***** KILL PED5552***** KILL PED5553***** KILL PED5558***** KILL PED5571***** KILL PED5574***** KILL PED5576***** KILL PED5582***** KILL PED5584***** KILL PED5585***** KILL PED5586***** KILL PED5592***** KILL PED5593***** KILL PED5594***** KILL PED5599***** KILL PED5607***** KILL PED5608***** KILL PED5619***** KILL PED5620***** KILL PED5629***** KILL PED5639***** KILL PED5642***** KILL PED5653***** KILL PED5661***** KILL PED5662***** KILL PED5666***** KILL PED5669***** KILL PED5670***** KILL PED5672***** KILL PED5676***** KILL PED5684***** KILL PED5697***** KILL PED5700***** KILL PED5718***** KILL PED5724***** KILL PED5725***** KILL PED5726***** KILL PED5727***** KILL PED5730***** KILL PED5731***** KILL PED5737***** KILL PED5738***** KILL PED5743***** KILL PED5749***** KILL PED5760***** KILL PED5768***** KILL PED5769***** KILL PED5781***** KILL PED5796***** KILL PED5798***** KILL PED5807***** KILL PED5812***** KILL PED5815***** KILL PED5816***** KILL PED5827***** KILL PED5866***** KILL PED5867***** KILL PED5868***** KILL PED5870***** KILL PED5871***** KILL PED5873***** KILL PED5900***** KILL PED5901***** KILL PED5911***** KILL PED5926***** KILL PED5928***** KILL PED5930***** KILL PED6035***** KILL PED6048***** KILL PED6049***** KILL 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*** TODO [[file:books.org::*The elements of statistical learning (217)][The elements of statistical learning (217)]] :**** TODO Chap 1-4**** TODO Chap 7-8*** TODO Introduction to statistical learning
*** STRT [[file:books.org::*The elements of statistical learning (217)][The elements of statistical learning (217)]] :**** STRT Chap 1-4**** Chap 7-8*** Introduction to statistical learning
*** TODO [[https://www.coursera.org/learn/machine-learning/home/info][Andrew NG coursera]]*** TODO The Deep Learning Book: https://www.deeplearningbook.org/front_matter.pdf*** TODO Put tensor flow or torch on a linux box and run examples: http://cs231n.github.io/aws-tutorial/
*** [[https://www.coursera.org/learn/machine-learning/home/info][Andrew NG coursera]]*** The Deep Learning Book: https://www.deeplearningbook.org/front_matter.pdf*** Put tensor flow or torch on a linux box and run examples: http://cs231n.github.io/aws-tutorial/
** Fixer rendez-vous* FreeBSD :freebsd:** KILL ormolu 0.5.0.0CLOSED: [2022-10-22 Sat 23:36] SCHEDULED: <2022-07-30 Sat>** Kitty*** KILL Problème sur fetchdirCLOSED: [2022-09-22 Thu 10:45]Commiter au courant, attente de résolution** WAIT [[https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=264158][pkgconf est trop lent sur freebsd]]Problème persiste avec dernière version
** TODO Collège [0/32]*** TODO 1. Architecture du génome*** TODO 2. Structure et fonction du génome humains: chromosomes sexuels*** TODO 3. Structure et fonction du génome humains*** TODO 4. Hérédité mendélienne*** TODO 5. Génétique des populations*** TODO 6. Cytogénétique conventionnelle*** TODO 7. Cytogénétique moléculaire*** TODO 8. Anomalies hémopathies et tumeurs solides
** Collège [0/32]*** 1. Architecture du génome*** 2. Structure et fonction du génome humains: chromosomes sexuels*** 3. Structure et fonction du génome humains*** 4. Hérédité mendélienne*** 5. Génétique des populations*** 6. Cytogénétique conventionnelle*** 7. Cytogénétique moléculaire*** 8. Anomalies hémopathies et tumeurs solides
*** TODO 11. Séquencage haut débit*** TODO 12. Conseil génétique*** TODO 13. Examen de l’enfant*** TODO 14. Hétérogénéite des maladies génétiques*** TODO 15. DPN, DPI*** TODO 16. Dépistage néonatal*** TODO 17. DPS*** TODO 18. Dispositions législatives*** TODO 19. Enjeux éthiques*** TODO 20. Maladies mitochondriales*** TODO 21. Empreinte parentale*** TODO 22. Mutations dynamiques*** TODO 23. Oncogénétique*** TODO 24. Bases de données*** TODO 25. Perspectives thérapeutiques*** TODO 26. Pharmacogénétique*** TODO 27. Génétique des maladies complexes*** TODO 28. T21*** TODO 29. Mucoviscidose*** TODO 30. Xfragile*** TODO 31. Maladies rares*** TODO 32. Médecine génomique
*** 11. Séquencage haut débit*** 12. Conseil génétique*** 13. Examen de l’enfant*** 14. Hétérogénéite des maladies génétiques*** 15. DPN, DPI*** 16. Dépistage néonatal*** 17. DPS*** 18. Dispositions législatives*** 19. Enjeux éthiques*** 20. Maladies mitochondriales*** 21. Empreinte parentale*** 22. Mutations dynamiques*** 23. Oncogénétique*** 24. Bases de données*** 25. Perspectives thérapeutiques*** 26. Pharmacogénétique*** 27. Génétique des maladies complexes*** 28. T21*** 29. Mucoviscidose*** 30. Xfragile*** 31. Maladies rares*** 32. Médecine génomique
*** TODO Fiche 18*** TODO Fiche 19*** TODO Fiche 20*** TODO Fiche 21*** TODO Fiche 22*** TODO Fiche 23*** TODO Fiche 24*** TODO Fiche 25*** TODO Fiche 26*** TODO Fiche 27*** TODO Fiche 28
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*** TODO Relire + notes [0/92]**** TODO Intro dysmorpho - Verloes**** TODO Empreinte génomique**** TODO Beckwith, Silver Russel**** TODO Scoliose**** TODO Syndromes cytogénétique - Salanville**** TODO Dysostose mandibulo faciale**** TODO Williams dup 7p11.2**** TODO Pathologie génétique de la reproduction**** TODO Malformations oculaires**** TODO Comprendre les test génétiques**** TODO Fente**** TODO Gonosome**** TODO Smith-Mangenis**** TODO 22q11**** TODO Dysmorpho nouveau-né**** TODO Autopsie foetale**** TODO Dysmorphologie - généralités (A Verloes)**** TODO Dysmorphologie du nouveau né (M Vincent)**** TODO Registre des malformations (N Lelong)**** TODO Comprendre les tests génétiques - Mutations - NGS (Y Vial)**** TODO Cytogénétique (C Missirian)**** TODO NGS et syndromologie (F Tran-Mau-Them)**** TODO Empreinte génomique (F Brioudé) (seq 15 Beckwith Wiedemann Syndrome et SRussel S)**** TODO Autopsie foetale (F Guimiot)**** TODO Tumeur et développement (H Cave)**** TODO Dysmorphologie foetale (MH Saint Frison)**** TODO Pathologie génétique de la reproduction (F Vialard)**** TODO Le dysmorphologiste en prénatal (N Gruchy)**** TODO Régulation génique et anomalies du développement (F Petit)**** TODO Echographie fœtale et dysmorphologie (C Rozel)**** TODO Déficience intellectuelle (A Curie)**** TODO Autisme et génétique (A Maruani)**** TODO Tests neuropsy**** TODO XLID(A Toutain)**** TODO Anomalies du développement embryonnaire précoce (C Quelin)**** TODO Anomalies de fermeture du tube neural (C Quelin)**** TODO FAS (D Germanaud)**** TODO Médicaments et grossesse (C Vauzelle)**** TODO Syndromes avec fentes oro-faciales- (J Van-Gils)**** TODO Syndromes avec craniosténose (C Collet)**** TODO Dents & syndromes (I Bailleul)**** TODO Dysostoses Mandibulo faciales (J Amiel)**** TODO Avances staturales (A Putoux)**** TODO Retards staturaux syndromiques (A Putoux)**** TODO Syndromes avec obésité (G Diene)**** TODO Spliceosomopathies (P Edery)**** TODO Microcéphalies (S Passemard)**** TODO Anomalies du cervelet : Joubert, NPH ... (L Burglen)**** TODO Epilepsie et syndromes (C Mignot)**** TODO Holoprosencéphalie (S Odent)**** TODO Hydrocephalie (S Odent)**** TODO Anomalies de migration (S Passemard)**** TODO Chondrodysplasies (G Baujat)**** TODO Anomalies de segmentation et scoliose (J Thévenon)**** TODO Génétique du développement des membres et principaux syndromes (F Petit)**** TODO Classification des malformations des membres (F Petit)**** TODO Prise en charge des anomalies des membres (N Quintero)**** TODO Syndromes avec anomalies uro-néphrologiques pré- et postnatal (G Morin)**** TODO Syndromes avec anomalies génitales et DSD (B Leheup)**** TODO Du coeur au syndrome (D Genevieve)**** TODO Malformation cardiaque en anténatal (D Genevieve)**** TODO Base génétique du déterminisme du sexe (C Colson)**** TODO Surdités syndromiques (S Marlin)**** TODO Malformations oculaires (N Chassaing)**** TODO Dermatologie et développement (P Vabres)**** TODO Dysmorphologie et métabolisme (M Barth)**** TODO Maladies de surcharge (D Germain)**** TODO Trisomie 21 (R Touraine)**** TODO S. Williams - duplication 7q11.2 (M Rossi)**** TODO Délétion 22q11.2 (L Perrin)**** TODO Syndromes cytogénétiques (D Sanlaville)**** TODO Gonosomes (J Leger)**** TODO Parcours de soin des patients avec anomalies du développement (N Jean-Marçais)**** TODO Prise en charge médicosociale du handicap (D Juzeau)**** TODO Fanconi (T Leblanc)**** TODO Ehlers-Danlos (D Germain)**** TODO Chromatinopathies: TAD - Kabuki, Rubinstein-Taybi, Wiedemann-Steiner, SBYSS... (D Genevieve)**** TODO Marfan et syndromes apparentés (G Jondeau)**** TODO RASopathies (Y Capri)**** TODO Syndromes de Pitt Hopkins, Angelman, Rett et Rett-like (N Bahi-Buisson)**** TODO Filaminopathies A (C Goizet)**** TODO Achondroplasie (G Baujat)**** TODO OI (G Baujat)**** TODO Ciliopathies: approche globale (T Attie-Bitach)**** TODO Smith-Magenis (L Perrin)**** TODO Cohésinopathies : Cornelia de Lange, Coffin-Siris/NB, CHOPS... (A Goldenberg)**** TODO Albinisme et syndromes apparentés (B Arveiler)**** TODO Beckwith Wiedemann Syndrome & Silver Russel Syndrome (F Brioude)**** TODO Neurofibromatoses - STB (C Goizet)**** TODO Cowden, Gorlin (P Goizet)**** TODO Syndrome de Kleefstra (L Perrin)**** TODO Téloméropathies (T Leblanc)
*** KILL Relire + notes [1/92]**** KILL Intro dysmorpho - VerloesCLOSED: [2023-07-07 Fri 18:43]**** KILL Empreinte génomique**** KILL Beckwith, Silver Russel**** KILL Scoliose**** KILL Syndromes cytogénétique - Salanville**** KILL Dysostose mandibulo faciale**** KILL Williams dup 7p11.2**** KILL Pathologie génétique de la reproduction**** KILL Malformations oculaires**** KILL Comprendre les test génétiques**** KILL Fente**** KILL Gonosome**** KILL Smith-Mangenis**** KILL 22q11**** KILL Dysmorpho nouveau-né**** KILL Autopsie foetale**** KILL Dysmorphologie - généralités (A Verloes)**** KILL Dysmorphologie du nouveau né (M Vincent)**** KILL Registre des malformations (N Lelong)**** KILL Comprendre les tests génétiques - Mutations - NGS (Y Vial)**** KILL Cytogénétique (C Missirian)**** KILL NGS et syndromologie (F Tran-Mau-Them)**** KILL Empreinte génomique (F Brioudé) (seq 15 Beckwith Wiedemann Syndrome et SRussel S)**** KILL Autopsie foetale (F Guimiot)**** KILL Tumeur et développement (H Cave)**** KILL Dysmorphologie foetale (MH Saint Frison)**** KILL Pathologie génétique de la reproduction (F Vialard)**** KILL Le dysmorphologiste en prénatal (N Gruchy)**** KILL Régulation génique et anomalies du développement (F Petit)**** KILL Echographie fœtale et dysmorphologie (C Rozel)**** KILL Déficience intellectuelle (A Curie)**** KILL Autisme et génétique (A Maruani)**** KILL Tests neuropsy**** KILL XLID(A Toutain)**** KILL Anomalies du développement embryonnaire précoce (C Quelin)**** KILL Anomalies de fermeture du tube neural (C Quelin)**** KILL FAS (D Germanaud)**** KILL Médicaments et grossesse (C Vauzelle)**** KILL Syndromes avec fentes oro-faciales- (J Van-Gils)**** KILL Syndromes avec craniosténose (C Collet)**** KILL Dents & syndromes (I Bailleul)**** KILL Dysostoses Mandibulo faciales (J Amiel)**** KILL Avances staturales (A Putoux)**** KILL Retards staturaux syndromiques (A Putoux)**** KILL Syndromes avec obésité (G Diene)**** KILL Spliceosomopathies (P Edery)**** KILL Microcéphalies (S Passemard)**** KILL Anomalies du cervelet : Joubert, NPH ... (L Burglen)**** KILL Epilepsie et syndromes (C Mignot)**** KILL Holoprosencéphalie (S Odent)**** KILL Hydrocephalie (S Odent)**** KILL Anomalies de migration (S Passemard)**** KILL Chondrodysplasies (G Baujat)**** KILL Anomalies de segmentation et scoliose (J Thévenon)**** KILL Génétique du développement des membres et principaux syndromes (F Petit)**** KILL Classification des malformations des membres (F Petit)**** KILL Prise en charge des anomalies des membres (N Quintero)**** KILL Syndromes avec anomalies uro-néphrologiques pré- et postnatal (G Morin)**** KILL Syndromes avec anomalies génitales et DSD (B Leheup)**** KILL Du coeur au syndrome (D Genevieve)**** KILL Malformation cardiaque en anténatal (D Genevieve)**** KILL Base génétique du déterminisme du sexe (C Colson)**** KILL Surdités syndromiques (S Marlin)**** KILL Malformations oculaires (N Chassaing)**** KILL Dermatologie et développement (P Vabres)**** KILL Dysmorphologie et métabolisme (M Barth)**** KILL Maladies de surcharge (D Germain)**** KILL Trisomie 21 (R Touraine)**** KILL S. Williams - duplication 7q11.2 (M Rossi)**** KILL Délétion 22q11.2 (L Perrin)**** KILL Syndromes cytogénétiques (D Sanlaville)**** KILL Gonosomes (J Leger)**** KILL Parcours de soin des patients avec anomalies du développement (N Jean-Marçais)**** KILL Prise en charge médicosociale du handicap (D Juzeau)**** KILL Fanconi (T Leblanc)**** KILL Ehlers-Danlos (D Germain)**** KILL Chromatinopathies: TAD - Kabuki, Rubinstein-Taybi, Wiedemann-Steiner, SBYSS... (D Genevieve)**** KILL Marfan et syndromes apparentés (G Jondeau)**** KILL RASopathies (Y Capri)**** KILL Syndromes de Pitt Hopkins, Angelman, Rett et Rett-like (N Bahi-Buisson)**** KILL Filaminopathies A (C Goizet)**** KILL Achondroplasie (G Baujat)**** KILL OI (G Baujat)**** KILL Ciliopathies: approche globale (T Attie-Bitach)**** KILL Smith-Magenis (L Perrin)**** KILL Cohésinopathies : Cornelia de Lange, Coffin-Siris/NB, CHOPS... (A Goldenberg)**** KILL Albinisme et syndromes apparentés (B Arveiler)**** KILL Beckwith Wiedemann Syndrome & Silver Russel Syndrome (F Brioude)**** KILL Neurofibromatoses - STB (C Goizet)**** KILL Cowden, Gorlin (P Goizet)**** KILL Syndrome de Kleefstra (L Perrin)**** KILL Téloméropathies (T Leblanc)
#+title: Bisonex* Biblio :biblio:** WorkflowComparaison WDL, Cromwell, nextflowhttps://www.nature.com/articles/s41598-021-99288-8Nextflow = bon compromis ?Comparison alignement, variant caller (2021)https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04144-1** Étapes du pipeline*** Variant calling: Haplotype callerhttps://gatk.broadinstitute.org/hc/en-us/articles/360035531412Définis l'algorithme + image*** Phred scorehttps://gatk.broadinstitute.org/hc/en-us/articles/360035531872-Phred-scaled-quality-scores** VCF*** GT genotypeencoded as alleles values separated by either of ”/” or “|”, e.g. The allele values are 0 for the reference allele (what is in the reference sequence), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on. For diploid calls examples could be 0/1 or 1|0 etc. For haploid calls, e.g. on Y, male X, mitochondrion, only one allele value should be given. All samples must have GT call information; if a call cannot be made for a sample at a given locus, ”.” must be specified for each missing allele in the GT field (for example ./. for a diploid). The meanings of the separators are:/ : genotype unphased| : genotype phased** Validation*** NA12878**** KILL [[https://precision.fda.gov/challenges/truth/results][fdaPrecision challenge]]Attention, génome et en hg19 donc comparaison non adaptée ...**** TODO Best practices for the analytical validation of clinical whole-genome sequencing intended for the diagnosis of germline diseasehttps://www.nature.com/articles/s41525-020-00154-9Recommandations générale pour genome, sans données brutes**** TODO [#A] Performance assessment of variant calling pipelines using human whole exome sequencing and simulated datahttps://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2928-91. variant calling seul2. NA12878 + données simulées3. exome4. évalué via F-scoreCode disponible ! https://github.com/bharani-lab/WES-Benchmarking-Pipeline_Manoj/tree/master/ScriptRésultat: BWA/Novoalign_DeepVariantAligneurs- BWA-MEM 0.7.16- Bowtie2 2.2.6- Novoalign 3.08.02- SOAP 2.21- MOSAIK 2.2.3Variantcalling- GATK HaplotypeCaller 4- FreeBayes 1.1.0- SAMtools mpileup 1.7- DeepVariant r0.4SNV| Exome | Pipeline | TP | FP | FN | Sensitivity | Precision | F-Score | FDR || 1 | BWA_GATK | 23689 | 1397 | 613 | 0.975 | 0.944 | 0.959 | 0.057 || 2 | BWA_GATK | 23946 | 865 | 356 | 0.985 | 0.965 | 0.975 | 0.036 |indel| TP | FP | FN | Sensitivity | Precision | F-Score | FDR | || 1254 | 72 | 75 | 0.944 | 0.946 | 0.945 | 0.054 | || 1309 | 10 | 20 | 0.985 | 0.992 | 0.989 | 0.008 | |Valeur brutes :https://static-content.springer.com/esm/art%3A10.1186%2Fs12859-019-2928-9/MediaObjects/12859_2019_2928_MOESM8_ESM.pdfAutres articles avec même comparaison en exome sur NA12878- Hwang et al., 2015 studyi- Highnam et al, 2015- Cornish and Guda, 2015Variant Type| | SNVs & Indels | CNVs (>10Kb) | SVs | Mitochondrial variants | Pseudogenes | REs | Somatic/ mosaic | Literature/Data | Source || NA12878 | 100%a | 40% | 0 | 0 | 0 | 0 | 0 | Zook et al18 | NIST || Other NIST standard | 71% | 40% | 50% | 0 | 0 | 0 | 0 | Zook et al18 | || (e.g. AJ/Asian trios) | | | | | | | | | || Platinum | 29% | 0 | 0 | 0 | 0 | 0 | 0 | Eberle et al8 | Platinum || Genomes | | | | | | | | | || Venter/HuRef | 14% | 40% | 0 | 0 | 0 | 0 | 0 | Trost et al1 | HuRef |**** Systematic comparison of germline variant calling pipelines cross multiple next-generation sequencers#+begin_src bibtex@ARTICLE{Chen2019-fp,title = "Systematic comparison of germline variant calling pipelinescross multiple next-generation sequencers",author = "Chen, Jiayun and Li, Xingsong and Zhong, Hongbin and Meng,Yuhuan and Du, Hongli",abstract = "The development and innovation of next generation sequencing(NGS) and the subsequent analysis tools have gain popularity inscientific researches and clinical diagnostic applications.Hence, a systematic comparison of the sequencing platforms andvariant calling pipelines could provide significant guidance toNGS-based scientific and clinical genomics. In this study, wecompared the performance, concordance and operating efficiencyof 27 combinations of sequencing platforms and variant callingpipelines, testing three variant calling pipelines-GenomeAnalysis Tool Kit HaplotypeCaller, Strelka2 andSamtools-Varscan2 for nine data sets for the NA12878 genomesequenced by different platforms including BGISEQ500,MGISEQ2000, HiSeq4000, NovaSeq and HiSeq Xten. For the variantscalling performance of 12 combinations in WES datasets, allcombinations displayed good performance in calling SNPs, withtheir F-scores entirely higher than 0.96, and their performancein calling INDELs varies from 0.75 to 0.91. And all 15combinations in WGS datasets also manifested good performance,with F-scores in calling SNPs were entirely higher than 0.975and their performance in calling INDELs varies from 0.71 to0.93. All of these combinations manifested high concordance invariant identification, while the divergence of variantsidentification in WGS datasets were larger than that in WESdatasets. We also down-sampled the original WES and WGS datasetsat a series of gradient coverage across multiple platforms, thenthe variants calling period consumed by the three pipelines ateach coverage were counted, respectively. For the GIAB datasetson both BGI and Illumina platforms, Strelka2 manifested itsultra-performance in detecting accuracy and processingefficiency compared with other two pipelines on each sequencingplatform, which was recommended in the further promotion andapplication of next generation sequencing technology. Theresults of our researches will provide useful and comprehensiveguidelines for personal or organizational researchers inreliable and consistent variants identification.",journal = "Sci. Rep.",publisher = "Springer Science and Business Media LLC",volume = 9,number = 1,pages = "9345",month = jun,year = 2019,copyright = "https://creativecommons.org/licenses/by/4.0",language = "en"}#+end_srcComparaison de différents pipeline 2019https://www.nature.com/articles/s41598-019-45835-3Combinaison- variant calling = GATK, Strelka2 and Samtools-Varscan2- sur NA12878- séquencé sur BGISEQ500, MGISEQ2000, HiSeq4000, NovaSeq and HiSeq Xten.Conclusion: strelka2 supérieur mais biais sur NA12878 ?Illumina > BGI pour indel, probablement car reads plus grand#+begin_quoteFor WES datasets, the BGI platforms displayed the superior performance in SNPscalling while Illumina platforms manifested the better variants callingperformance in INDELs calling, which could
#+title: Bisonex#+FILETAGS: @bisonex* Biblio :biblio:** WorkflowComparaison WDL, Cromwell, nextflowhttps://www.nature.com/articles/s41598-021-99288-8Nextflow = bon compromis ?Comparison alignement, variant caller (2021)https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04144-1** Étapes du pipeline*** Variant calling: Haplotype callerhttps://gatk.broadinstitute.org/hc/en-us/articles/360035531412Définis l'algorithme + image*** Phred scorehttps://gatk.broadinstitute.org/hc/en-us/articles/360035531872-Phred-scaled-quality-scores** VCF*** GT genotypeencoded as alleles values separated by either of ”/” or “|”, e.g. The allele values are 0 for the reference allele (what is in the reference sequence), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on. For diploid calls examples could be 0/1 or 1|0 etc. For haploid calls, e.g. on Y, male X, mitochondrion, only one allele value should be given. All samples must have GT call information; if a call cannot be made for a sample at a given locus, ”.” must be specified for each missing allele in the GT field (for example ./. for a diploid). The meanings of the separators are:/ : genotype unphased| : genotype phased** Validation*** NA12878**** KILL [[https://precision.fda.gov/challenges/truth/results][fdaPrecision challenge]]Attention, génome et en hg19 donc comparaison non adaptée ...**** TODO Best practices for the analytical validation of clinical whole-genome sequencing intended for the diagnosis of germline diseasehttps://www.nature.com/articles/s41525-020-00154-9Recommandations générale pour genome, sans données brutes**** TODO [#A] Performance assessment of variant calling pipelines using human whole exome sequencing and simulated datahttps://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2928-91. variant calling seul2. NA12878 + données simulées3. exome4. évalué via F-scoreCode disponible ! https://github.com/bharani-lab/WES-Benchmarking-Pipeline_Manoj/tree/master/ScriptRésultat: BWA/Novoalign_DeepVariantAligneurs- BWA-MEM 0.7.16- Bowtie2 2.2.6- Novoalign 3.08.02- SOAP 2.21- MOSAIK 2.2.3Variantcalling- GATK HaplotypeCaller 4- FreeBayes 1.1.0- SAMtools mpileup 1.7- DeepVariant r0.4SNV| Exome | Pipeline | TP | FP | FN | Sensitivity | Precision | F-Score | FDR || 1 | BWA_GATK | 23689 | 1397 | 613 | 0.975 | 0.944 | 0.959 | 0.057 || 2 | BWA_GATK | 23946 | 865 | 356 | 0.985 | 0.965 | 0.975 | 0.036 |indel| TP | FP | FN | Sensitivity | Precision | F-Score | FDR | || 1254 | 72 | 75 | 0.944 | 0.946 | 0.945 | 0.054 | || 1309 | 10 | 20 | 0.985 | 0.992 | 0.989 | 0.008 | |Valeur brutes :https://static-content.springer.com/esm/art%3A10.1186%2Fs12859-019-2928-9/MediaObjects/12859_2019_2928_MOESM8_ESM.pdfAutres articles avec même comparaison en exome sur NA12878- Hwang et al., 2015 studyi- Highnam et al, 2015- Cornish and Guda, 2015Variant Type| | SNVs & Indels | CNVs (>10Kb) | SVs | Mitochondrial variants | Pseudogenes | REs | Somatic/ mosaic | Literature/Data | Source || NA12878 | 100%a | 40% | 0 | 0 | 0 | 0 | 0 | Zook et al18 | NIST || Other NIST standard | 71% | 40% | 50% | 0 | 0 | 0 | 0 | Zook et al18 | || (e.g. AJ/Asian trios) | | | | | | | | | || Platinum | 29% | 0 | 0 | 0 | 0 | 0 | 0 | Eberle et al8 | Platinum || Genomes | | | | | | | | | || Venter/HuRef | 14% | 40% | 0 | 0 | 0 | 0 | 0 | Trost et al1 | HuRef |**** Systematic comparison of germline variant calling pipelines cross multiple next-generation sequencers#+begin_src bibtex@ARTICLE{Chen2019-fp,title = "Systematic comparison of germline variant calling pipelinescross multiple next-generation sequencers",author = "Chen, Jiayun and Li, Xingsong and Zhong, Hongbin and Meng,Yuhuan and Du, Hongli",abstract = "The development and innovation of next generation sequencing(NGS) and the subsequent analysis tools have gain popularity inscientific researches and clinical diagnostic applications.Hence, a systematic comparison of the sequencing platforms andvariant calling pipelines could provide significant guidance toNGS-based scientific and clinical genomics. In this study, wecompared the performance, concordance and operating efficiencyof 27 combinations of sequencing platforms and variant callingpipelines, testing three variant calling pipelines-GenomeAnalysis Tool Kit HaplotypeCaller, Strelka2 andSamtools-Varscan2 for nine data sets for the NA12878 genomesequenced by different platforms including BGISEQ500,MGISEQ2000, HiSeq4000, NovaSeq and HiSeq Xten. For the variantscalling performance of 12 combinations in WES datasets, allcombinations displayed good performance in calling SNPs, withtheir F-scores entirely higher than 0.96, and their performancein calling INDELs varies from 0.75 to 0.91. And all 15combinations in WGS datasets also manifested good performance,with F-scores in calling SNPs were entirely higher than 0.975and their performance in calling INDELs varies from 0.71 to0.93. All of these combinations manifested high concordance invariant identification, while the divergence of variantsidentification in WGS datasets were larger than that in WESdatasets. We also down-sampled the original WES and WGS datasetsat a series of gradient coverage across multiple platforms, thenthe variants calling period consumed by the three pipelines ateach coverage were counted, respectively. For the GIAB datasetson both BGI and Illumina platforms, Strelka2 manifested itsultra-performance in detecting accuracy and processingefficiency compared with other two pipelines on each sequencingplatform, which was recommended in the further promotion andapplication of next generation sequencing technology. Theresults of our researches will provide useful and comprehensiveguidelines for personal or organizational researchers inreliable and consistent variants identification.",journal = "Sci. Rep.",publisher = "Springer Science and Business Media LLC",volume = 9,number = 1,pages = "9345",month = jun,year = 2019,copyright = "https://creativecommons.org/licenses/by/4.0",language = "en"}#+end_srcComparaison de différents pipeline 2019https://www.nature.com/articles/s41598-019-45835-3Combinaison- variant calling = GATK, Strelka2 and Samtools-Varscan2- sur NA12878- séquencé sur BGISEQ500, MGISEQ2000, HiSeq4000, NovaSeq and HiSeq Xten.Conclusion: strelka2 supérieur mais biais sur NA12878 ?Illumina > BGI pour indel, probablement car reads plus grand#+begin_quoteFor WES datasets, the BGI platforms displayed the superior performance in SNPscalling while Illumina platforms manifested the better variants callingperformance in INDELs calling, which could
py2conda install -c bioconda hap.py#+end_src******** Faire tourner les tests.Il faut remplace bin/test_haplotypes par test_haplotypes dans src/sh/run_tests.sh#+begin_src shHGREF=../genome/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta HCDIR=~/anaconda3/envs/py2/bin bash src/sh/run_tests.sh#+end_srcEchec:test_haplotypes: /opt/conda/conda-bld/work/hap.py-0.3.7/src/c++/lib/tools/Fasta.cpp:81: MMappedFastaFile::MMappedFastaFile(const string&): Assertion `fd != -1' failed.unknown location(0): fatal error in "testVariantPrimitiveSplitter": signal: SIGABRT (application abort requested)/opt/conda/conda-bld/work/hap.py-0.3.7/src/c++/test/test_align.cpp(298): last checkpoint******** Chr21HGREF=../genome/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta hap.py example/happy/PG_NA12878_chr21.vcf.gz example/happy/NA12878_chr21.vcf.gz -f example/happy/PG_Conf_chr21.bed.gz -o test******* Helioséchec** TODO T2T :T2T:Toutes les ressourcs sont décrites icihttps://github.com/marbl/CHM13Détails sur le pipelinehttps://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hub_3267197_GCA_009914755.4&c=CP068277.2&g=hub_3267197_hgLiftOver*** DONE AlignementCLOSED: [2023-06-26 Mon 19:42]NXF_OPTS=-D"user.name=${USER}" nextflow run main.nf -profile standard,helios --input="/Work/Groups/bisonex/data/giab/*_R{1,2}_001.fastq.gz" --id=NA12878-T2T -bgSCHEDULED: <2023-06-14 Wed>*** DONE HaplotypecallerCLOSED: [2023-06-26 Mon 19:42] SCHEDULED: <2023-06-15 Thu>*** TODO FiltresSCHEDULED: <2023-07-10 Mon>*** Liftover pipelines:PROPERTIES::ID: d2280207-3f65-4a31-a291-41fa9a9658c2:END:Contient les chain files** TODO Indicateurs qualitéSCHEDULED: <2023-07-07 Fri>*** IdéeRaredisease:- FastQC : nombreuses statistiques. Non disponible Nix- Mosdepth : calcule la profondeur (2x plus rapide que samtools depth). Nix- MultiQC : fusionne juste les résultats des analyses. Non disponible nix- Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics- Qualimap : alternative fastqc ? Non disponible nix- Sentieon's WgsMetricsAlgo : propriétaire- TIDDIT's cov : TIDIT = remaninement chromosomiqueSarek:- alignment statistics : samtools stats, mosdepth- QC : MultiQCMultiQC : non disponible Nix** TODO vérifier si normalisationSCHEDULED: <2023-07-08 Sat>** TODO Rajouter vérification hgvsSCHEDULED: <2023-07-08 Sat>** DONE ExécutionCLOSED: [2022-09-13 Tue 21:37]*** KILL test Bionix*** KILL Implémenter execution avec Nix ?Voir https://academic.oup.com/gigascience/article/9/11/giaa121/5987272?login=falsepour un exemple.Probablement plus simple d’utiliser Nix pour gestion de l’environnement et snakemake pour l’exécutionPas d’accès internet depuis le cluster*** DONE nextflowCLOSED: [2022-09-13 Tue 21:37]**** TODO Bug scheduler SGELe job se fait tuer car l'utilisateur n'est pas passé correctement à nextflow***** DONE Forcer l'utilisateur à l'exécutionCLOSED: [2023-04-01 Sat 17:57]NXF_OPTS=-D"user.name=alex"***** DONE Vérifier si le problème persiste avec 22.10.6CLOSED: [2023-04-01 Sat 18:38] SCHEDULED: <2023-04-01 Sat>oui***** KILL Packager l'utilisateur dans le programme ?Mauvaise idée..** TODO Preprocessing avec nextflow*** TODO Map to reference**** TODO Sample ID dans header/Work/Users/apraga/bisonex/out/63003856_S135/preprocessing/baserecalibrator*** DONE Mark duplicateCLOSED: [2022-10-09 Sun 22:30]*** DONE Recalibrate base quality scoreCLOSED: [2022-10-09 Sun 22:30]** DONE Variant calling avec NextflowCLOSED: [2022-11-19 Sat 21:34]*** DONE Haplotype callerCLOSED: [2022-10-09 Sun 22:40]*** DONE Filter variantsCLOSED: [2022-10-09 Sun 22:40]*** DONE Filter common snp not clinvar pathCLOSED: [2022-11-07 Mon 23:00]Voir [[*common dbSNP not clinvar patho][common dbSNP not clinvar patho]]*** DONE Filter variant only in consensual sequenceCLOSED: [2022-11-08 Tue 22:23]*** DONE Filter technical variantsCLOSED: [2022-11-19 Sat 21:34]*** DONE Utilise AVX pour accélerer l'exécutionCLOSED: [2023-04-29 Sat 15:46]Sans cela, on a l'avertissement#+begin_quote17:28:00.720 INFO PairHMM - OpenMP multi-threaded AVX-accelerated native PairHMM implementation is not supported17:28:00.721 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/nix/store/cy9ckxqwrkifx7wf02hm4ww1p6lnbxg9-gatk-4.2.4.1/bin/gatk-package-4.2.4.1-local.jar!/com/intel/gkl/native/libgkl_utils.so17:28:00.733 WARN NativeLibraryLoader - Unable to load libgkl_utils.so from native/libgkl_utils.so (/Work/Users/apraga/bisonex/out/NA12878_NIST7035/preprocessing/applybqsr/libgkl_utils821485189051585397.so: libgomp.so.1: cannot open shared object file: No such file or directory)17:28:00.733 WARN IntelPairHmm - Intel GKL Utils not loaded17:28:00.733 WARN PairHMM - ***WARNING: Machine does not have the AVX instruction set support needed for the accelerated AVX PairHmm. Falling back to the MUCH slower LOGLESS_CACHING implementation!17:28:00.763 INFO ProgressMeter - Starting traversal#+end_quotelibgomp.so est fourni par gcc donc il faut charger le modulemodule load gcc@11.3.0/gcc-12.1.0** KILL Utiliser subworkflowCLOSED: [2023-04-02 Sun 18:08]Notre version permet d'être plus souple*** KILL AlignementCLOSED: [2023-04-02 Sun 18:08] SCHEDULED: <2023-04-05 Wed>*** KILL VepCLOSED: [2023-04-02 Sun 18:08] SCHEDULED: <2023-04-05 Wed>vcf_annotate_ensemblvep** TODO Annotation avec nextflow :annotation:*** KILL VEP : --gene-phenotype ?CLOSED: [2023-04-18 mar. 18:32]Vu avec alexis : bases de données non à jourhttps://www.ensembl.org/info/genome/variation/phenotype/sources_phenotype_documentation.html*** DONE plugin VEPCLOSED: [2023-04-18 mar. 18:32]Cloner dépôt git avec pluginPuis utiliser --dir_plugins*** HOLD Utiliser code d’Alexis*** TODO Nouvelle version avec VEPExample avec --customhttps://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html**** DONE Ajout spliceAICLOSED: [2023-05-18 Thu 11:02] SCHEDULED: <2023-04-30 Sun>plugin VEP***** DONE Télécharger les donnéesCLOSED: [2023-05-11 Thu 19:01]Difficile d'automatiser, le lien est temporaire...***** DONE PLuginCLOSED: [2023-05-11 Thu 20:16]***** DONE Séparer score en plusieurs colonnesCLOSED: [2023-05-11 Thu 20:16]Test avec ce fichier pour avoir une ligne avec annotation et une ligne sans#CHROM POS ID REF ALT1 9091 . A C1 69091 . A Cet#+begin_src shrm -f postvep.tsv* && vep -i testspliceai.vcf.gz -o postvep.tsv --tab --dir 109 --merged --pick --use_given_ref --offline --plugin SpliceAI,snv=spliceai_scores.raw.snv.hg38.vcf.gz,indel=spliceai_scores.raw.indel.hg38.vcf.gz#+end_src#+begin_src$ bgzip postvep.tsv$ python spliceai.py$ cat postvep2.tsv,variation,Location,Allele,Gene,Feature,Feature_type,Consequence,cDNA_position,CDS_position,Protein_position,Amino_acids,Codons,Existing_variation,IMPACT,DISTANCE,STRAND,FLAGS,REFSEQ_MATCH,SOURCE,REFSEQ_OFFSET,SpliceAI_AG,SpliceAI_AL,SpliceAI_DG,SpliceAI_DL0,1_9091_A/C,1:9091,C,ENSG00000290825,ENST00000456328,Transcript,upstream_gene_variant,-,-,-,-,-,-,MODIFIER,2778,1,-,-,Ensembl,-,,,,1,1_69091_A/C,1:69091,C,ENSG00000186092,ENST00000641515,Transcript,missense_variant,124,64,22,M/L,Atg/Ctg,-,MODERATE,-,1,-,-,Ensembl,-,0.01,0.00,0.00,0.01#+end_srcTestcp work/bf/437ae511958509e43072f032f4d495/small.tab.gz tests/vep-spip.tab.gzcp work/d5/3b1244b5ae83d54409ee0d456e8c55/small_cadd.tab.gz tests/vep-cadd-splice.tab.gz**** TODO Ajout LOEUF et pliplugin VEP**** TODO NMD**** KILL Ajout LOEUFCLOSED: [2023-04-19 mer. 16:32]plugin VEP**** DONE SpipCLOSED: [2023-05-01 Mon 23:07] SCHEDULED: <2023-04-30 Sun>BED ne semble pas bien marcher (il faut définir une zone)VCF : trop d’informationAttention, plusieurs transcripts mais résultats identiques. On supprimer les doublons***** DONE interpretation + score + intervalle de confiance séparéCLOSED: [2023-05-01 Mon 23:07] SCHEDULED: <2023-04-30 Sun>Tests :dans tests/vep -i 630049
py2conda install -c bioconda hap.py#+end_src******** Faire tourner les tests.Il faut remplace bin/test_haplotypes par test_haplotypes dans src/sh/run_tests.sh#+begin_src shHGREF=../genome/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta HCDIR=~/anaconda3/envs/py2/bin bash src/sh/run_tests.sh#+end_srcEchec:test_haplotypes: /opt/conda/conda-bld/work/hap.py-0.3.7/src/c++/lib/tools/Fasta.cpp:81: MMappedFastaFile::MMappedFastaFile(const string&): Assertion `fd != -1' failed.unknown location(0): fatal error in "testVariantPrimitiveSplitter": signal: SIGABRT (application abort requested)/opt/conda/conda-bld/work/hap.py-0.3.7/src/c++/test/test_align.cpp(298): last checkpoint******** Chr21HGREF=../genome/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta hap.py example/happy/PG_NA12878_chr21.vcf.gz example/happy/NA12878_chr21.vcf.gz -f example/happy/PG_Conf_chr21.bed.gz -o test******* Helioséchec** TODO T2T :T2T:Toutes les ressourcs sont décrites icihttps://github.com/marbl/CHM13Détails sur le pipelinehttps://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hub_3267197_GCA_009914755.4&c=CP068277.2&g=hub_3267197_hgLiftOver*** DONE AlignementCLOSED: [2023-06-26 Mon 19:42]NXF_OPTS=-D"user.name=${USER}" nextflow run main.nf -profile standard,helios --input="/Work/Groups/bisonex/data/giab/*_R{1,2}_001.fastq.gz" --id=NA12878-T2T -bgSCHEDULED: <2023-06-14 Wed>*** DONE HaplotypecallerCLOSED: [2023-06-26 Mon 19:42] SCHEDULED: <2023-06-15 Thu>*** TODO FiltresSCHEDULED: <2023-07-10 Mon>*** Liftover pipelines:PROPERTIES::ID: d2280207-3f65-4a31-a291-41fa9a9658c2:END:Contient les chain files** TODO Indicateurs qualitéSCHEDULED: <2023-07-14 Fri>*** IdéeRaredisease:- FastQC : nombreuses statistiques. Non disponible Nix- Mosdepth : calcule la profondeur (2x plus rapide que samtools depth). Nix- MultiQC : fusionne juste les résultats des analyses. Non disponible nix- Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics- Qualimap : alternative fastqc ? Non disponible nix- Sentieon's WgsMetricsAlgo : propriétaire- TIDDIT's cov : TIDIT = remaninement chromosomiqueSarek:- alignment statistics : samtools stats, mosdepth- QC : MultiQCMultiQC : non disponible Nix** TODO vérifier si normalisationSCHEDULED: <2023-07-14 Fri>** TODO Rajouter vérification hgvsSCHEDULED: <2023-07-14 Fri>** DONE ExécutionCLOSED: [2022-09-13 Tue 21:37]*** KILL test Bionix*** KILL Implémenter execution avec Nix ?Voir https://academic.oup.com/gigascience/article/9/11/giaa121/5987272?login=falsepour un exemple.Probablement plus simple d’utiliser Nix pour gestion de l’environnement et snakemake pour l’exécutionPas d’accès internet depuis le cluster*** DONE nextflowCLOSED: [2022-09-13 Tue 21:37]**** TODO Bug scheduler SGELe job se fait tuer car l'utilisateur n'est pas passé correctement à nextflow***** DONE Forcer l'utilisateur à l'exécutionCLOSED: [2023-04-01 Sat 17:57]NXF_OPTS=-D"user.name=alex"***** DONE Vérifier si le problème persiste avec 22.10.6CLOSED: [2023-04-01 Sat 18:38] SCHEDULED: <2023-04-01 Sat>oui***** KILL Packager l'utilisateur dans le programme ?Mauvaise idée..** TODO Preprocessing avec nextflow*** TODO Map to reference**** TODO Sample ID dans header/Work/Users/apraga/bisonex/out/63003856_S135/preprocessing/baserecalibrator*** DONE Mark duplicateCLOSED: [2022-10-09 Sun 22:30]*** DONE Recalibrate base quality scoreCLOSED: [2022-10-09 Sun 22:30]** DONE Variant calling avec NextflowCLOSED: [2022-11-19 Sat 21:34]*** DONE Haplotype callerCLOSED: [2022-10-09 Sun 22:40]*** DONE Filter variantsCLOSED: [2022-10-09 Sun 22:40]*** DONE Filter common snp not clinvar pathCLOSED: [2022-11-07 Mon 23:00]Voir [[*common dbSNP not clinvar patho][common dbSNP not clinvar patho]]*** DONE Filter variant only in consensual sequenceCLOSED: [2022-11-08 Tue 22:23]*** DONE Filter technical variantsCLOSED: [2022-11-19 Sat 21:34]*** DONE Utilise AVX pour accélerer l'exécutionCLOSED: [2023-04-29 Sat 15:46]Sans cela, on a l'avertissement#+begin_quote17:28:00.720 INFO PairHMM - OpenMP multi-threaded AVX-accelerated native PairHMM implementation is not supported17:28:00.721 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/nix/store/cy9ckxqwrkifx7wf02hm4ww1p6lnbxg9-gatk-4.2.4.1/bin/gatk-package-4.2.4.1-local.jar!/com/intel/gkl/native/libgkl_utils.so17:28:00.733 WARN NativeLibraryLoader - Unable to load libgkl_utils.so from native/libgkl_utils.so (/Work/Users/apraga/bisonex/out/NA12878_NIST7035/preprocessing/applybqsr/libgkl_utils821485189051585397.so: libgomp.so.1: cannot open shared object file: No such file or directory)17:28:00.733 WARN IntelPairHmm - Intel GKL Utils not loaded17:28:00.733 WARN PairHMM - ***WARNING: Machine does not have the AVX instruction set support needed for the accelerated AVX PairHmm. Falling back to the MUCH slower LOGLESS_CACHING implementation!17:28:00.763 INFO ProgressMeter - Starting traversal#+end_quotelibgomp.so est fourni par gcc donc il faut charger le modulemodule load gcc@11.3.0/gcc-12.1.0** KILL Utiliser subworkflowCLOSED: [2023-04-02 Sun 18:08]Notre version permet d'être plus souple*** KILL AlignementCLOSED: [2023-04-02 Sun 18:08] SCHEDULED: <2023-04-05 Wed>*** KILL VepCLOSED: [2023-04-02 Sun 18:08] SCHEDULED: <2023-04-05 Wed>vcf_annotate_ensemblvep** TODO Annotation avec nextflow :annotation:*** KILL VEP : --gene-phenotype ?CLOSED: [2023-04-18 mar. 18:32]Vu avec alexis : bases de données non à jourhttps://www.ensembl.org/info/genome/variation/phenotype/sources_phenotype_documentation.html*** DONE plugin VEPCLOSED: [2023-04-18 mar. 18:32]Cloner dépôt git avec pluginPuis utiliser --dir_plugins*** HOLD Utiliser code d’Alexis*** TODO Nouvelle version avec VEPExample avec --customhttps://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html**** DONE Ajout spliceAICLOSED: [2023-05-18 Thu 11:02] SCHEDULED: <2023-04-30 Sun>plugin VEP***** DONE Télécharger les donnéesCLOSED: [2023-05-11 Thu 19:01]Difficile d'automatiser, le lien est temporaire...***** DONE PLuginCLOSED: [2023-05-11 Thu 20:16]***** DONE Séparer score en plusieurs colonnesCLOSED: [2023-05-11 Thu 20:16]Test avec ce fichier pour avoir une ligne avec annotation et une ligne sans#CHROM POS ID REF ALT1 9091 . A C1 69091 . A Cet#+begin_src shrm -f postvep.tsv* && vep -i testspliceai.vcf.gz -o postvep.tsv --tab --dir 109 --merged --pick --use_given_ref --offline --plugin SpliceAI,snv=spliceai_scores.raw.snv.hg38.vcf.gz,indel=spliceai_scores.raw.indel.hg38.vcf.gz#+end_src#+begin_src$ bgzip postvep.tsv$ python spliceai.py$ cat postvep2.tsv,variation,Location,Allele,Gene,Feature,Feature_type,Consequence,cDNA_position,CDS_position,Protein_position,Amino_acids,Codons,Existing_variation,IMPACT,DISTANCE,STRAND,FLAGS,REFSEQ_MATCH,SOURCE,REFSEQ_OFFSET,SpliceAI_AG,SpliceAI_AL,SpliceAI_DG,SpliceAI_DL0,1_9091_A/C,1:9091,C,ENSG00000290825,ENST00000456328,Transcript,upstream_gene_variant,-,-,-,-,-,-,MODIFIER,2778,1,-,-,Ensembl,-,,,,1,1_69091_A/C,1:69091,C,ENSG00000186092,ENST00000641515,Transcript,missense_variant,124,64,22,M/L,Atg/Ctg,-,MODERATE,-,1,-,-,Ensembl,-,0.01,0.00,0.00,0.01#+end_srcTestcp work/bf/437ae511958509e43072f032f4d495/small.tab.gz tests/vep-spip.tab.gzcp work/d5/3b1244b5ae83d54409ee0d456e8c55/small_cadd.tab.gz tests/vep-cadd-splice.tab.gz**** TODO Ajout LOEUF et pliplugin VEP**** TODO NMD**** KILL Ajout LOEUFCLOSED: [2023-04-19 mer. 16:32]plugin VEP**** DONE SpipCLOSED: [2023-05-01 Mon 23:07] SCHEDULED: <2023-04-30 Sun>BED ne semble pas bien marcher (il faut définir une zone)VCF : trop d’informationAttention, plusieurs transcripts mais résultats identiques. On supprimer les doublons***** DONE interpretation + score + intervalle de confiance séparéCLOSED: [2023-05-01 Mon 23:07] SCHEDULED: <2023-04-30 Sun>Tests :dans tests/vep -i 630049
/On utilisé les données "trimmés" (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1069-7), i.e qui ont enlevé les fragments plus petits que la taille d'un read.Informations:- https://ftp-trace.ncbi.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/Garvan_NA12878_HG001_HiSeq_Exome.README- Sequencer: HiSeq2500- kit: Nextera Rapid Capture Exome and Expanded ExomeIl y a 2 samples (NIST7035 et NIST7086), chacun sur 2 lanes -> à concaténerNB : liste techno illumina https://www.illumina.com/systems/sequencing-platforms.htmlHiseq postérieur nextseq 550******* TODO Fastq hiseq sans trimming******* DONE Capture : Exons (bed)CLOSED: [2023-02-25 Sat 19:46]https://ftp-trace.ncbi.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/nexterarapidcapture_expandedexome_targetedregions.bed.gz******* DONE Bed, vcfCLOSED: [2023-02-24 Fri 23:45]****** DONE Ashkenazy trio HG002, HG003, HGQ004CLOSED: [2023-04-06 Thu 21:43] SCHEDULED: <2023-04-01 Sat>****** KILL Chinese trio HG005, 6, 7CLOSED: [2023-04-16 Sun 16:32]***** KILL Fastq :fastq:CLOSED: [2023-04-16 Sun 16:32]****** DONE NA12878 (HG001)CLOSED: [2023-02-25 Sat 19:46]******* DONE Fastq HiSeqCLOSED: [2023-02-25 Sat 19:46]On prend le Hiseq, qui est probablement ce qu'utilise Centogène :https://ftp-trace.ncbi.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/On utilisé les données "trimmés" (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1069-7), i.e qui ont enlevé les fragments plus petits que la taille d'un read.Informations:- https://ftp-trace.ncbi.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/Garvan_NA12878_HG001_HiSeq_Exome.README- Sequencer: HiSeq2500- kit: Nextera Rapid Capture Exome and Expanded ExomeIl y a 2 samples (NIST7035 et NIST7086), chacun sur 2 lanes -> à concaténerNB : liste techno illumina https://www.illumina.com/systems/sequencing-platforms.htmlHiseq postérieur nextseq 550******* DONE Capture : Exons (bed)CLOSED: [2023-02-25 Sat 19:46]https://ftp-trace.ncbi.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/nexterarapidcapture_expandedexome_targetedregions.bed.gz****** DONE Ashkenazy trio HG002, HG003, HG004CLOSED: [2023-04-15 Sat 23:24] SCHEDULED: <2023-04-05 Wed>******* DONE CaptureCLOSED: [2023-04-15 Sat 23:24]https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/OsloUniversityHospital_Exome_GATK_jointVC_11242015/wex_Agilent_SureSelect_v05_b37.baits.slop50.merged.list******* DONE Capture AgilentCLOSED: [2023-04-15 Sat 23:24]******* DONE Bam à partir des fastqCLOSED: [2023-04-15 Sat 23:24]Bam + index + checksumhttps://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/AshkenazimTrio/alignment.index.AJtrio_OsloUniversityHospital_IlluminaExome_bwamem_GRCh37_11252015****** KILL Chinese trioCLOSED: [2023-04-16 Sun 16:32]Whole exome pour HG005 seulement******* KILL HG005CLOSED: [2023-04-16 Sun 16:32]https://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/ChineseTrio/alignment.index.Chinesetrio_HG005_OsloUniversityHospital_IlluminaExome_bwamem_GRCh37_11252015**** DONE Télécharger FASTQ directement avec aws (via SRA)CLOSED: [2023-06-30 Fri 22:30] SCHEDULED: <2023-06-27 Tue>***** RemarquesNuméro d'accession : https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08365-3/tables/1Fastq disponible via SRA. Avec AWS, on peut accéder au fastq directement.(Sinon il faut convertir SRA -> Fastq avec le toolkit : compliqué à configurer)Exemple: https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR2962669&display=data-accessAvantage:- pas de conversion BAM -> fASTQ- détail des capture- capture en hg38 sur site du constructeur !!- capture semblable pour ashkenaziInconvénient :- NA12878 : discordance pour le nombre de paires de bases : NA12878 = 49G (donc 24G de fastq)- capture non disponible en ligne (site agilent)- format SRA (le lien pour les fastq n'est pas gratuit): utiliser HTTP ou leur toolkit (télécharge au format SRA puis convertit en fastq). Exemple: pour avoir 2 fastqfastq-dump --split-files --gzip SRR2962669***** Liste des runs :https://www.ncbi.nlm.nih.gov/sraCherche avec numéro patient. On a le choix entre plusieurs séquenceurs Illumina- NovaSeq 6000 TruSeq capture SRX11061536- NovaSeq 6000 IDT capture SRX11061526- NovaSeq 6000 Agilent SureSelect v7 capture SRX11061516- HiSeq 4000 TruSeq capture SRX11061506- HiSeq 4000 IDT capture SRX11061496- HiSeq 4000 Agilent SureSelect v7 capture SRX11061486Note: SRX = expérience, SRR = runImportant:- ne pas compresser la sortie avec fasta-dump directement (lent++)- Fasterq-dump est plus rapideNote trueseq non disponible ?hg19 : https://www.biostars.org/p/144554/IDT: lequelhttps://www.idtdna.com/pages/products/next-generation-sequencing/workflow/xgen-ngs-hybridization-capture/pre-designed-hyb-cap-panels/exome-hyb-panel-v2***** DONE HiSeq 4000 + agilent sureselect :sra:CLOSED: [2023-06-28 Wed 22:06] SCHEDULED: <2023-06-28 Wed>- [ ] HG001 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061486 SRR14724513- [ ] HG002 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061487 SRR14724512- [ ] HG003 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061488 SRR14724511- [ ] HG004 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061489 SRR14724510Other- HG005 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061491 SRR14724508- HG006 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061492 SRR14724507- HG007 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061493 SRR14724506******* DONE Capture agilent sureselectCLOSED: [2023-06-30 Fri 22:30] SCHEDULED: <2023-06-28 Wed>**** TODO Lift T2T :T2T:#+begin_quoteWe performed liftover using the GATK release 4.1.9 LiftoverVcf (Picard Version 2.23.3) tool with the default parameters. This successfully lifts over variants that map exactly from GRCh38 to T2T-CHM13v2.0 but does not recover variants with swapped reference and alternative alleles. To recover variants with swapped reference/alternative alleles, we ran LiftoverVCF again, with the RECOVER_SWAPPED_REF_ALT flag. Notably, this feature does not recover multiallelic variants, so to recover these variants, we first separated them into multiple biallelic variants, performed liftover using the RECOVER_SWAPPED_REF_ALT tag, and converted them back to their multiallelic representations.#+end_quote***** KILL Liftovervcf avec valeur par défautCLOSED: [2023-07-02 Sun 23:09] SCHEDULED: <2023-06-30 Fri>HG002 : il manque la moitié des valeurshg001[apraga@mesointeractive b946d0e6bc8d0f220eb1ad1649c20d]$ less HG004_GRCh38_1_22_v4.2.1_benchmark.vcf.lifted.vcf.gz[apraga@mesointeractive b946d0e6bc8d0f220eb1ad1649c20d]$ zgrep -c '^chr' HG004_GRCh38_1_22_v4.2.1_benchmark.vcf.lifted.vcf.gz2168972[apraga@mesointeractive b946d0e6bc8d0f220eb1ad1649c20d]$ zgrep -c '^chr' HG004_GRCh38_1_22_v4.2.1_benchmark.vcf.unlifted.vcf.gz1862374[apraga@mesointeractive b946d0e6bc8d0f220eb1ad1649c20d]$ zgrep -c '^chr' HG004_GRCh38_1_22_v4.2.1_benchmark.vcf.gz4031346***** DONE liftover bedCLOSED: [2023-07-02 Sun 23:09] SCHEDULED: <2023-06-30 Fri>792 of 217488 intervals failed (0.364158%) to liftover, encompassing 219109 of 35718732 bases (0.613429%).wc -l capture/Agilent_SureSelect_All_Exons_v7_hg38_Regions.bed217488 capture/Agilent_SureSelect_All_Exons_v7_hg38_Regions.bedwc -l work/e4/9981dc539a2373c2beeaa0affc3497/Agilent_SureSelect_All_Exons_v7_hg38_Regions_hg38.interval_listOn a donc perdu 1000 zones***** DONE Liftovervcf avec variant échangé référence/alternative ?CLOSED: [2023-07-02 Sun 23:09]***** TODO Comprendre pourquoi HG001 ne passe plusSCHEDULED: <2023-07-03 Mon>****** TODO Comparer hg38 et T2T: 2x moinsr de variants, trop de FP et FNT2T| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio || INDEL | ALL | 413 | 246 | 167 | 751 | 289 | 215 | 2 | 93 | 0.595642 | 0.460821 | 0.286285 | 0.519629 | NaN | NaN | 2.428571 | 2.465116 || INDEL | PASS | 413 | 246 | 167 | 751 | 289 | 215 | 2 | 93 | 0.595642 | 0.460821 | 0.286285 | 0.519629 | NaN | NaN | 2.428571 | 2.465116 || SNP | ALL | 11236 | 10985 | 251 | 23597 | 9771 | 2841 | 26 | 58 | 0.977661 | 0.529245 | 0.120397 | 0.686734 | 3.11461 | 2.85705 | 3.640644 | 2.114633 || SNP | PASS | 11236 | 10985 | 251 | 23597 | 9771 | 2841 | 26 | 58 | 0.977661 | 0.529245 | 0.120397 | 0.686734 | 3.11461 | 2.85705 | 3.640644 | 2.114633 |Hg38| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio || INDEL | ALL | 549 | 489 | 60 | 899 | 64 | 340 | 8 | 17 | 0.890710 | 0.885510 | 0.378198 | 0.888102 | NaN | NaN | 1.860963 | 2.247273 || INDEL | PASS | 549 | 489 | 60 | 899 | 64 | 340 | 8 | 17 | 0.890710 | 0.885510 | 0.378198 | 0.888102 | NaN | NaN | 1.860963 | 2.247273 || SNP | ALL | 21973 | 21462 | 511 | 26285 | 563 | 4263 | 68 | 16 | 0.976744 | 0.974435 | 0.162184 | 0.975588 | 3.00711 | 2.784686 | 1.591810 | 1.816145 || SNP | PASS | 21973 | 21462 | 511 | 26285 | 563 | 4263 | 68 | 16 | 0.976744 | 0.974435 | 0.162184 | 0.975588 | 3.00711 | 2.784686 | 1.591810 | 1.816145 |******* RésuméT2T| Type | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision || INDEL | 413 | 246 | 167 | 751 | 289 | 215 | 2 | 93 | 0.595642 | 0.460821 || SNP | 11236 | 10985 | 251 | 23597 | 9771 | 2841 | 26 | 58 | 0.977661 | 0.529245 |Hg38| Type | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision || INDEL | 549 | 489 | 60 | 899 | 64 | 340 | 8 | 17 | 0.890710 | 0.885510 || SNP | 21973 | 21462 | 511 | 26285 | 563 | 4263 | 68 | 16 | 0.976744 | 0.974435 |****** TODO Comparer quelques FP et FN****** DONE Interesection des bed: similaireCLOSED: [2023-07-04 Tue 23:11]HG38#+begin_src shbedtools intersect -a capture/Agilent_SureSelect_All_Exons_v7_hg38_Regions.bed -b /Work/Groups/bisonex/data/giab/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.bed | wc -l#+end_src204280T2T#+begin_src shbedtools intersect -a /Work/Groups/bisonex/data/giab/T2T/Agilent_SureSelect_All_Exons_v7_hg38_Regions_hg38_T2T.bed -b /Work/Groups/bisonex/data/giab/T2T/HG001_GRCh38_1_22_v4.2.1_benchmark_hg38_T2T.bed | wc -l#+end_src204021****** DONE Vérifier la ligne de commandeCLOSED: [2023-07-04 Tue 23:38]#+begin_src shhap.py \HG001_GRCh38_1_22_v4_lifted_merged.vcf.gz \HG001-SRX11061486_SRR14724513-T2T.vcf.gz \\--reference chm13v2.0.fa \--threads 6 \\-T Agilent_SureSelect_All_Exons_v7_hg38_Regions_hg38_T2T.bed \--false-positives HG001_GRCh38_1_22_v4.2.1_benchmark_hg38_T2T.bed \\-o HG001#+end_src**** DONE NA12878 :na12878:hg38:CLOSED: [2023-06-30 Fri 22:30]***** DONE Discussion alexis : MailCLOSED: [2023-03-29 Wed 22:40]Avec le patient NA12878 et comparaison avec hap.py du VCF de Genome In A Bottle ("gold" standard), on avait pour rappel- sensibilité (=recall) 71% pour indel, 85% SNP- précision (= VPP) 69 et 97% respectivement| Type | TRUTH | TP | FN | QUERY | FP | UNK | FP.gt | FP.al | Recall | Precision || INDEL | 4871 | 3461 | 1410 | 7048 | 1554 | 1987 | 193 | 346 | 0.710532 | 0.692946 || SNP | 46032 | 39369 | 6663 | 44600 | 1186 | 4041 | 304 | 30 | 0.855253 | 0.970759 |Les statistiques sur les génomes sont bien meilleurs (cf precisionFDA challenge).Pour les exome, un article [1] a fait a des meilleures stats sur ce patient avec BWA et GATK mais ils ont moins de variant (on a presque un facteur 2 !).Je soupçonne qu'on ne travaille pas sur les mêmes zones de capture (pas réussi à récupérer leur .bed)| Exome | Type | TP | FP | FN | Sensitivity | Precision | F-Score | FDR || 1 | SNV | 23689 | 1397 | 613 | 0.975 | 0.944 | 0.959 | 0.057 || 2 | SNV | 23946 | 865 | 356 | 0.985 | 0.965 | 0.975 | 0.036 || 1 | indel | 1254 | 72 | 75 | 0.944 | 0.946 | 0.945 | 0.054 || 2 | indel | 1309 | 10 | 20 | 0.985 | 0.992 | 0.989 | 0.008 |Pour essayer d'améliorer les statistiques :- La version du génome GRC38 vs GRCh38.p13 ne change quasiment rien- Désactiver dbSNP ne change strictement rien pour le variant callingJ'ai exploré les faux négatifs :- la grande majorité n'est juste pas vue (ce n'est pas un problème d'haploïde/génotype)- la répartition par chromosome est relativement homogène, sauf sur le 6 ()- la majorité est en 5' et 3'UTR (selon Best refseq)Conclusion: je pense m'arrêter là pour la validation du variant calling par manque de temps. Il faudrait creuser pour savoir pourquoi certains variants ne sont pas vus par GATK mais ce n'est pas la majorité. En tout cas, je peux justifier d'une première analyse pour la thèse.Ça te va ?[1]https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2928-9Résultats ici https://static-content.springer.com/esm/art%3A10.1186%2Fs12859-019-2928-9/MediaObjects/12859_2019_2928_MOESM8_ESM.pdf***** DONE ComparaisonCLOSED: [2023-03-04 Sat 11:14]HGREF=/Work/Groups/bisonex/data-alexis-reference/genome/GRCh38_latest_genomic.fna ./result/bin/hap.py /Work/Groups/bisonex/NA12878/HG001_GRCh38_1_22_v4.2.1_benchmark_renamed.vcf.gz script/files/vcf/NA12878_NIST7035_vep_annot.vcf -f /Work/Groups/bisonex/NA12878/HG001_GRCh38_1_22_v4.2.1_benchmark.bed -o testna1878.slurm#+begin_src slurm#!/bin/bash#SBATCH -c 4#SBATCH -p smp#SBATCH --time=01:00:00#SBATCH --mem=32Gmodule load nix/2.11.0export HGREF=/Work/Groups/bisonex/data-alexis-reference/genome/GRCh38_latest_genomic.fnadir=/Work/Groups/bisonex/data/NA12878/GRCh38hap.py ${dir}/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz script/files/vcf/NA12878_NIST7035.vcf -f ${dir}/HG001_GRCh38_1_22_v4.2.1_benchmark.bed -o test#+end_src****** KILL beaucoup trop de faux négatifsCLOSED: [2023-02-17 Fri 19:37]******* DONE Test 1 : vep annot : beaucoup trop de faux
/On utilisé les données "trimmés" (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1069-7), i.e qui ont enlevé les fragments plus petits que la taille d'un read.Informations:- https://ftp-trace.ncbi.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/Garvan_NA12878_HG001_HiSeq_Exome.README- Sequencer: HiSeq2500- kit: Nextera Rapid Capture Exome and Expanded ExomeIl y a 2 samples (NIST7035 et NIST7086), chacun sur 2 lanes -> à concaténerNB : liste techno illumina https://www.illumina.com/systems/sequencing-platforms.htmlHiseq postérieur nextseq 550******* TODO Fastq hiseq sans trimming******* DONE Capture : Exons (bed)CLOSED: [2023-02-25 Sat 19:46]https://ftp-trace.ncbi.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/nexterarapidcapture_expandedexome_targetedregions.bed.gz******* DONE Bed, vcfCLOSED: [2023-02-24 Fri 23:45]****** DONE Ashkenazy trio HG002, HG003, HGQ004CLOSED: [2023-04-06 Thu 21:43] SCHEDULED: <2023-04-01 Sat>****** KILL Chinese trio HG005, 6, 7CLOSED: [2023-04-16 Sun 16:32]***** KILL Fastq :fastq:CLOSED: [2023-04-16 Sun 16:32]****** DONE NA12878 (HG001)CLOSED: [2023-02-25 Sat 19:46]******* DONE Fastq HiSeqCLOSED: [2023-02-25 Sat 19:46]On prend le Hiseq, qui est probablement ce qu'utilise Centogène :https://ftp-trace.ncbi.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/On utilisé les données "trimmés" (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1069-7), i.e qui ont enlevé les fragments plus petits que la taille d'un read.Informations:- https://ftp-trace.ncbi.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/Garvan_NA12878_HG001_HiSeq_Exome.README- Sequencer: HiSeq2500- kit: Nextera Rapid Capture Exome and Expanded ExomeIl y a 2 samples (NIST7035 et NIST7086), chacun sur 2 lanes -> à concaténerNB : liste techno illumina https://www.illumina.com/systems/sequencing-platforms.htmlHiseq postérieur nextseq 550******* DONE Capture : Exons (bed)CLOSED: [2023-02-25 Sat 19:46]https://ftp-trace.ncbi.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/nexterarapidcapture_expandedexome_targetedregions.bed.gz****** DONE Ashkenazy trio HG002, HG003, HG004CLOSED: [2023-04-15 Sat 23:24] SCHEDULED: <2023-04-05 Wed>******* DONE CaptureCLOSED: [2023-04-15 Sat 23:24]https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/OsloUniversityHospital_Exome_GATK_jointVC_11242015/wex_Agilent_SureSelect_v05_b37.baits.slop50.merged.list******* DONE Capture AgilentCLOSED: [2023-04-15 Sat 23:24]******* DONE Bam à partir des fastqCLOSED: [2023-04-15 Sat 23:24]Bam + index + checksumhttps://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/AshkenazimTrio/alignment.index.AJtrio_OsloUniversityHospital_IlluminaExome_bwamem_GRCh37_11252015****** KILL Chinese trioCLOSED: [2023-04-16 Sun 16:32]Whole exome pour HG005 seulement******* KILL HG005CLOSED: [2023-04-16 Sun 16:32]https://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/ChineseTrio/alignment.index.Chinesetrio_HG005_OsloUniversityHospital_IlluminaExome_bwamem_GRCh37_11252015**** DONE Télécharger FASTQ directement avec aws (via SRA)CLOSED: [2023-06-30 Fri 22:30] SCHEDULED: <2023-06-27 Tue>***** RemarquesNuméro d'accession : https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08365-3/tables/1Fastq disponible via SRA. Avec AWS, on peut accéder au fastq directement.(Sinon il faut convertir SRA -> Fastq avec le toolkit : compliqué à configurer)Exemple: https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR2962669&display=data-accessAvantage:- pas de conversion BAM -> fASTQ- détail des capture- capture en hg38 sur site du constructeur !!- capture semblable pour ashkenaziInconvénient :- NA12878 : discordance pour le nombre de paires de bases : NA12878 = 49G (donc 24G de fastq)- capture non disponible en ligne (site agilent)- format SRA (le lien pour les fastq n'est pas gratuit): utiliser HTTP ou leur toolkit (télécharge au format SRA puis convertit en fastq). Exemple: pour avoir 2 fastqfastq-dump --split-files --gzip SRR2962669***** Liste des runs :https://www.ncbi.nlm.nih.gov/sraCherche avec numéro patient. On a le choix entre plusieurs séquenceurs Illumina- NovaSeq 6000 TruSeq capture SRX11061536- NovaSeq 6000 IDT capture SRX11061526- NovaSeq 6000 Agilent SureSelect v7 capture SRX11061516- HiSeq 4000 TruSeq capture SRX11061506- HiSeq 4000 IDT capture SRX11061496- HiSeq 4000 Agilent SureSelect v7 capture SRX11061486Note: SRX = expérience, SRR = runImportant:- ne pas compresser la sortie avec fasta-dump directement (lent++)- Fasterq-dump est plus rapideNote trueseq non disponible ?hg19 : https://www.biostars.org/p/144554/IDT: lequelhttps://www.idtdna.com/pages/products/next-generation-sequencing/workflow/xgen-ngs-hybridization-capture/pre-designed-hyb-cap-panels/exome-hyb-panel-v2***** DONE HiSeq 4000 + agilent sureselect :sra:CLOSED: [2023-06-28 Wed 22:06] SCHEDULED: <2023-06-28 Wed>- [ ] HG001 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061486 SRR14724513- [ ] HG002 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061487 SRR14724512- [ ] HG003 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061488 SRR14724511- [ ] HG004 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061489 SRR14724510Other- HG005 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061491 SRR14724508- HG006 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061492 SRR14724507- HG007 with Illumina HiSeq 4000 Agilent SureSelect v7 capture SRX11061493 SRR14724506******* DONE Capture agilent sureselectCLOSED: [2023-06-30 Fri 22:30] SCHEDULED: <2023-06-28 Wed>**** TODO Lift T2T :T2T:#+begin_quoteWe performed liftover using the GATK release 4.1.9 LiftoverVcf (Picard Version 2.23.3) tool with the default parameters. This successfully lifts over variants that map exactly from GRCh38 to T2T-CHM13v2.0 but does not recover variants with swapped reference and alternative alleles. To recover variants with swapped reference/alternative alleles, we ran LiftoverVCF again, with the RECOVER_SWAPPED_REF_ALT flag. Notably, this feature does not recover multiallelic variants, so to recover these variants, we first separated them into multiple biallelic variants, performed liftover using the RECOVER_SWAPPED_REF_ALT tag, and converted them back to their multiallelic representations.#+end_quote***** KILL Liftovervcf avec valeur par défautCLOSED: [2023-07-02 Sun 23:09] SCHEDULED: <2023-06-30 Fri>HG002 : il manque la moitié des valeurshg001[apraga@mesointeractive b946d0e6bc8d0f220eb1ad1649c20d]$ less HG004_GRCh38_1_22_v4.2.1_benchmark.vcf.lifted.vcf.gz[apraga@mesointeractive b946d0e6bc8d0f220eb1ad1649c20d]$ zgrep -c '^chr' HG004_GRCh38_1_22_v4.2.1_benchmark.vcf.lifted.vcf.gz2168972[apraga@mesointeractive b946d0e6bc8d0f220eb1ad1649c20d]$ zgrep -c '^chr' HG004_GRCh38_1_22_v4.2.1_benchmark.vcf.unlifted.vcf.gz1862374[apraga@mesointeractive b946d0e6bc8d0f220eb1ad1649c20d]$ zgrep -c '^chr' HG004_GRCh38_1_22_v4.2.1_benchmark.vcf.gz4031346***** DONE liftover bedCLOSED: [2023-07-02 Sun 23:09] SCHEDULED: <2023-06-30 Fri>792 of 217488 intervals failed (0.364158%) to liftover, encompassing 219109 of 35718732 bases (0.613429%).wc -l capture/Agilent_SureSelect_All_Exons_v7_hg38_Regions.bed217488 capture/Agilent_SureSelect_All_Exons_v7_hg38_Regions.bedwc -l work/e4/9981dc539a2373c2beeaa0affc3497/Agilent_SureSelect_All_Exons_v7_hg38_Regions_hg38.interval_listOn a donc perdu 1000 zones***** DONE Liftovervcf avec variant échangé référence/alternative ?CLOSED: [2023-07-02 Sun 23:09]***** TODO Comprendre mauvais résultatSCHEDULED: <2023-07-03 Mon>****** TODO Beaucoup trop de FPSCHEDULED: <2023-07-07 Fri>******* TODO Répartition des FP : cluster ?******* TODO Examiner quelques FP******* TODO Méthodologie du pangenome******* TODO [#A] Certains FP sont des vrais FP: erreur d'happy ?SCHEDULED: <2023-07-07 Fri>****** TODO 2x moins de variants****** DONE Comparer hg38 et T2T: 2x moinsr de variants, trop de FP et FNCLOSED: [2023-07-07 Fri 18:38]T2T| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio || INDEL | ALL | 413 | 246 | 167 | 751 | 289 | 215 | 2 | 93 | 0.595642 | 0.460821 | 0.286285 | 0.519629 | NaN | NaN | 2.428571 | 2.465116 || INDEL | PASS | 413 | 246 | 167 | 751 | 289 | 215 | 2 | 93 | 0.595642 | 0.460821 | 0.286285 | 0.519629 | NaN | NaN | 2.428571 | 2.465116 || SNP | ALL | 11236 | 10985 | 251 | 23597 | 9771 | 2841 | 26 | 58 | 0.977661 | 0.529245 | 0.120397 | 0.686734 | 3.11461 | 2.85705 | 3.640644 | 2.114633 || SNP | PASS | 11236 | 10985 | 251 | 23597 | 9771 | 2841 | 26 | 58 | 0.977661 | 0.529245 | 0.120397 | 0.686734 | 3.11461 | 2.85705 | 3.640644 | 2.114633 |Hg38| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio || INDEL | ALL | 549 | 489 | 60 | 899 | 64 | 340 | 8 | 17 | 0.890710 | 0.885510 | 0.378198 | 0.888102 | NaN | NaN | 1.860963 | 2.247273 || INDEL | PASS | 549 | 489 | 60 | 899 | 64 | 340 | 8 | 17 | 0.890710 | 0.885510 | 0.378198 | 0.888102 | NaN | NaN | 1.860963 | 2.247273 || SNP | ALL | 21973 | 21462 | 511 | 26285 | 563 | 4263 | 68 | 16 | 0.976744 | 0.974435 | 0.162184 | 0.975588 | 3.00711 | 2.784686 | 1.591810 | 1.816145 || SNP | PASS | 21973 | 21462 | 511 | 26285 | 563 | 4263 | 68 | 16 | 0.976744 | 0.974435 | 0.162184 | 0.975588 | 3.00711 | 2.784686 | 1.591810 | 1.816145 |******* RésuméT2T| Type | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision || INDEL | 413 | 246 | 167 | 751 | 289 | 215 | 2 | 93 | 0.595642 | 0.460821 || SNP | 11236 | 10985 | 251 | 23597 | 9771 | 2841 | 26 | 58 | 0.977661 | 0.529245 |Hg38| Type | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision || INDEL | 549 | 489 | 60 | 899 | 64 | 340 | 8 | 17 | 0.890710 | 0.885510 || SNP | 21973 | 21462 | 511 | 26285 | 563 | 4263 | 68 | 16 | 0.976744 | 0.974435 |****** DONE Interesection des bed: similaireCLOSED: [2023-07-04 Tue 23:11]HG38#+begin_src shbedtools intersect -a capture/Agilent_SureSelect_All_Exons_v7_hg38_Regions.bed -b /Work/Groups/bisonex/data/giab/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.bed | wc -l#+end_src204280T2T#+begin_src shbedtools intersect -a /Work/Groups/bisonex/data/giab/T2T/Agilent_SureSelect_All_Exons_v7_hg38_Regions_hg38_T2T.bed -b /Work/Groups/bisonex/data/giab/T2T/HG001_GRCh38_1_22_v4.2.1_benchmark_hg38_T2T.bed | wc -l#+end_src204021****** DONE Vérifier la ligne de commandeCLOSED: [2023-07-04 Tue 23:38]#+begin_src shhap.py \HG001_GRCh38_1_22_v4_lifted_merged.vcf.gz \HG001-SRX11061486_SRR14724513-T2T.vcf.gz \\--reference chm13v2.0.fa \--threads 6 \\-T Agilent_SureSelect_All_Exons_v7_hg38_Regions_hg38_T2T.bed \--false-positives HG001_GRCh38_1_22_v4.2.1_benchmark_hg38_T2T.bed \\-o HG001#+end_src***** TODO Mail Yannis***** DONE Mail GIAB pour version T2TCLOSED: [2023-07-07 Fri 18:37]**** DONE NA12878 :na12878:hg38:CLOSED: [2023-06-30 Fri 22:30]***** DONE Discussion alexis : MailCLOSED: [2023-03-29 Wed 22:40]Avec le patient NA12878 et comparaison avec hap.py du VCF de Genome In A Bottle ("gold" standard), on avait pour rappel- sensibilité (=recall) 71% pour indel, 85% SNP- précision (= VPP) 69 et 97% respectivement| Type | TRUTH | TP | FN | QUERY | FP | UNK | FP.gt | FP.al | Recall | Precision || INDEL | 4871 | 3461 | 1410 | 7048 | 1554 | 1987 | 193 | 346 | 0.710532 | 0.692946 || SNP | 46032 | 39369 | 6663 | 44600 | 1186 | 4041 | 304 | 30 | 0.855253 | 0.970759 |Les statistiques sur les génomes sont bien meilleurs (cf precisionFDA challenge).Pour les exome, un article [1] a fait a des meilleures stats sur ce patient avec BWA et GATK mais ils ont moins de variant (on a presque un facteur 2 !).Je soupçonne qu'on ne travaille pas sur les mêmes zones de capture (pas réussi à récupérer leur .bed)| Exome | Type | TP | FP | FN | Sensitivity | Precision | F-Score | FDR || 1 | SNV | 23689 | 1397 | 613 | 0.975 | 0.944 | 0.959 | 0.057 || 2 | SNV | 23946 | 865 | 356 | 0.985 | 0.965 | 0.975 | 0.036 || 1 | indel | 1254 | 72 | 75 | 0.944 | 0.946 | 0.945 | 0.054 || 2 | indel | 1309 | 10 | 20 | 0.985 | 0.992 | 0.989 | 0.008 |Pour essayer d'améliorer les statistiques :- La version du génome GRC38 vs GRCh38.p13 ne change quasiment rien- Désactiver dbSNP ne change strictement rien pour le variant callingJ'ai exploré les faux négatifs :- la grande majorité n'est juste pas vue (ce n'est pas un problème d'haploïde/génotype)- la répartition par chromosome est relativement homogène, sauf sur le 6 ()- la majorité est en 5' et 3'UTR (selon Best refseq)Conclusion: je pense m'arrêter là pour la validation du variant calling par manque de temps. Il faudrait creuser pour savoir pourquoi certains variants ne sont pas vus par GATK mais ce n'est pas la majorité. En tout cas, je peux justifier d'une première analyse pour la thèse.Ça te va ?[1]https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2928-9Résultats ici https://static-content.springer.com/esm/art%3A10.1186%2Fs12859-019-2928-9/MediaObjects/12859_2019_2928_MOESM8_ESM.pdf***** DONE ComparaisonCLOSED: [2023-03-04 Sat 11:14]HGREF=/Work/Groups/bisonex/data-alexis-reference/genome/GRCh38_latest_genomic.fna ./result/bin/hap.py /Work/Groups/bisonex/NA12878/HG001_GRCh38_1_22_v4.2.1_benchmark_renamed.vcf.gz script/files/vcf/NA12878_NIST7035_vep_annot.vcf -f /Work/Groups/bisonex/NA12878/HG001_GRCh38_1_22_v4.2.1_benchmark.bed -o testna1878.slurm#+begin_src slurm#!/bin/bash#SBATCH -c 4#SBATCH -p smp#SBATCH --time=01:00:00#SBATCH --mem=32Gmodule load nix/2.11.0export HGREF=/Work/Groups/bisonex/data-alexis-reference/genome/GRCh38_latest_genomic.fnadir=/Work/Groups/bisonex/data/NA12878/GRCh38hap.py ${dir}/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz script/files/vcf/NA12878_NIST7035.vcf -f ${dir}/HG001_GRCh38_1_22_v4.2.1_benchmark.bed -o test#+end_src****** KILL beaucoup trop de faux négatifsCLOSED: [2023-02-17 Fri 19:37]******* DONE Test 1 : vep annot : beaucoup trop de faux
ld | True-pos-baseline | True-pos-call | False-pos | False-neg | Precision | Sensitivity | F-measure ||-----------+-------------------+---------------+-----------+-----------+-----------+-------------+-----------|| 3.000 | 42789 | 42416 | 2598 | 8080 | 0.9423 | 0.8412 | 0.8889 || None | 42798 | 42425 | 2616 | 8071 | 0.9419 | 0.8413 | 0.8888 |Indel avec le plus petit seuil : zcat NA12878.non_snp_roc.tsv.gzAttention à inverser precision et recall !zcat NA12878.non_snp_roc.tsv.gz | tail -n 1 | awk '{print $7 $6}'0.71390.7136SNP avec le plus petit seuil : zcat NA12878.non_snp_roc.tsv.gzAttention à inverser precision et recall !$ zcat NA12878.snp_roc.tsv.gz | tail -n 1 | awk '{print $7 $6}'0.85470.9727compareNA12878-giab/vcfeval/NA12878.summary.txt| Threshold | True-pos-baseline | True-pos-call | False-pos | False-neg | Precision | Sensitivity | F-measure || 1.000 | 44812 | 44812 | 2878 | 6057 | 0.9397 | 0.8809 | 0.9093 || None | 44813 | 44813 | 2882 | 6056 | 0.9396 | 0.8809 | 0.9093 |SNP:$ zcat NA12878.snp_roc.tsv.gz | tail -n 1 | awk '{print $7 $6}'0.89370.9621indel$ zcat NA12878.non_snp_roc.tsv.gz | tail -n 1 | awk '{print $7 $6}'0.75980.7445compareNA12878-giab/happy/NA12878.summary.csv| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio ||-------+--------+-------------+----------+----------+-------------+----------+-----------+-------+-------+---------------+------------------+----------------+-----------------+------------------------+------------------------+---------------------------+---------------------------|| INDEL | ALL | 4871 | 3678 | 1193 | 7036 | 1299 | 2011 | 208 | 217 | 0.755081 | 0.741493 | 0.285816 | 0.748225 | | | 1.6174985978687606 | 2.5240506329113925 || INDEL | PASS | 4871 | 3678 | 1193 | 7036 | 1299 | 2011 | 208 | 217 | 0.755081 | 0.741493 | 0.285816 | 0.748225 | | | 1.6174985978687606 | 2.5240506329113925 || SNP | ALL | 46032 | 41138 | 4894 | 47694 | 1622 | 4930 | 362 | 31 | 0.893683 | 0.962071 | 0.103367 | 0.926617 | 2.529551552318896 | 2.4124463519313304 | 1.6206857273037931 | 1.6888675840288743 || SNP | PASS | 46032 | 41138 | 4894 | 47694 | 1622 | 4930 | 362 | 31 | 0.893683 | 0.962071 | 0.103367 | 0.926617 | 2.529551552318896 | 2.4124463519313304 | 1.6206857273037931 | 1.688867584028874 |***** KILL Résultats sans trimmingCLOSED: [2023-06-25 Sun 15:53] SCHEDULED: <2023-06-26 Mon>***** DONE Refaire : HiSeq4000 + agilent sureselect + génome "prêt à l'emploi"CLOSED: [2023-06-30 Fri 22:08] SCHEDULED: <2023-06-25 Sun>#+begin_srcnextflow run workflows/compareVCF.nf -profile standard,helios --outdir=out/HG001-SRX11061486_SRR14724513-GRCh38 --query=out/HG001-SRX11061486_SRR14724513-GRCh38/callVariant/haplotypecaller/HG001-SRX11061486_SRR14724513-GRCh38.vcf.gz --compare=vcfeval,happy -lib lib --capture=capture/Agilent_SureSelect_All_Exons_v7_hg38_Regions.bed --id=HG001#+end_srcMeilleurs résultats !| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio || INDEL | ALL | 549 | 489 | 60 | 899 | 64 | 340 | 8 | 17 | 0.89071 | 0.88551 | 0.378198 | 0.888102 | | | 1.86096256684492 | 2.247272727272727 || INDEL | PASS | 549 | 489 | 60 | 899 | 64 | 340 | 8 | 17 | 0.89071 | 0.88551 | 0.378198 | 0.888102 | | | 1.86096256684492 | 2.247272727272727 || SNP | ALL | 21973 | 21462 | 511 | 26285 | 563 | 4263 | 68 | 16 | 0.976744 | 0.974435 | 0.162184 | 0.975588 | 3.007110300820419 | 2.78468624064479 | 1.5918102430965306 | 1.8161449399656946 || SNP | PASS | 21973 | 21462 | 511 | 26285 | 563 | 4263 | 68 | 16 | 0.976744 | 0.974435 | 0.162184 | 0.975588 | 3.007110300820419 | 2.78468624064479 | 1.5918102430965306 | 1.8161449399656946 |***** KILL Utiliser d'autres données brutes ?CLOSED: [2023-06-25 Sun 15:58]https://zenodo.org/record/3597727Capture en hg37 également. Serait intéressant mais pas le temps..***** KILL Comparer avec UCSCS liftoverCLOSED: [2023-06-26 Mon 19:02] SCHEDULED: <2023-06-25 Sun>Picard liftoverinterval est basé sur UCSCSMais on n'aurait pas la différence pour NA12878 qu'on voit...**** TODO HG002 :hg002:hg38:SCHEDULED: <2023-04-10 Mon>#+begin_srcNXF_OPTS=-D"user.name=${USER}" nextflow run workflows/giabFastq.nf -profile standard,heliosNXF_OPTS=-D"user.name=${USER}" nextflow run main.nf -profile standard,helios -resume --input="/Work/Groups/bisonex/data/giab/GRCh38/HG002_{1,2}.fq.gz --test.id=HG002Only the capture file differs. Results are better using the capture file given by Agilent, stored in data/NXF_OPTS=-D"user.name=${USER}" nextflow run workflows/compareVCF.nf -profile standard,helios -resume --outdir=compareHG002 --test.id=HG002 --test.query=out/HG002_1/variantCalling/haplotypecaller/HG002_1.vcf.gz --test.compare=vcfeval,happy --test.capture=data/AgilentSureSelectv05_hg38.bed##+end_src***** DONE Mauvais résultatsCLOSED: [2023-04-14 Fri 09:42]avec vcfevalThreshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure----------------------------------------------------------------------------------------------------0.000 24585 24390 10060 39415 0.7080 0.3841 0.4980None 24585 24390 10060 39415 0.7080 0.3841 0.4980La sortie du variantCalling est celle d'happy ???On relance...***** DONE Vérifier vcf en hg38CLOSED: [2023-04-12 Wed 10:33] SCHEDULED: <2023-04-12 Wed>***** KILL Capture en hg19 ?CLOSED: [2023-04-13 Thu 09:46] SCHEDULED: <2023-04-12 Wed>***** KILL Vraiment fichier de capture ou zone d'intérêt ?CLOSED: [2023-04-13 Thu 09:45] SCHEDULED: <2023-04-12 Wed>"target region" +/- 50bp[[https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/analysis/OsloUniversityHospital_Exome_GATK_jointVC_11242015/README.txt][README]]list file describing the variant calling regions (target regions extended with 50 bp on each end)***** DONE .bed fourni par AGilent: sensbilité très mauvaiseCLOSED: [2023-04-13 Thu 09:46] SCHEDULED: <2023-04-13 Thu>Agilent SureSelect Human All Exon V5 kitDisponible en hg38Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure----------------------------------------------------------------------------------------------------0.000 19653 19501 6410 21657 0.7526 0.4757 0.5830None 19653 19501 6410 21657 0.7526 0.4757 0.5830***** DONE Trier par nom avec samtools sort : bons résultatsCLOSED: [2023-04-14 Fri 09:25] SCHEDULED: <2023-04-13 Thu>Avec capture fourni par GIABvcf evalThreshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure----------------------------------------------------------------------------------------------------5.000 57443 57032 984 6557 0.9830 0.8975 0.9383None 57457 57046 1009 6543 0.9826 0.8978 0.9383Happy| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall| METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio ||-------+--------+-------------+----------+----------+-------------+----------+-----------+-------+-------+---------------+------------------+----------------+-----------------+------------------------+------------------------+---------------------------+---------------------------|| INDEL | ALL | 6150 | 5007 | 1143 | 6978 | 556 | 1346 | 151 | 168 | 0.814146 | 0.901278 | 0.192892 | 0.8555 | | | 1.5434221840068787 | 1.9467178175618074 || INDEL | PASS | 6150 | 5007 | 1143 | 6978 | 556 | 1346 | 151 | 168 | 0.814146 | 0.901278 | 0.192892 | 0.8555 | | | 1.5434221840068787 | 1.9467178175618074 || SNP | ALL | 57818 | 52464 | 5354 | 56016 | 500 | 3046 | 90 | 30 | 0.907399 | 0.990561 | 0.054377 | 0.947158 | 2.4892012548262548 | 2.426824047458871 | 1.5904527117884357 | 1.6107795598657217 || SNP | PASS | 57818 | 52464 | 5354 | 56016 | 500 | 3046 | 90 | 30 | 0.907399 | 0.990561 | 0.054377 | 0.947158 | 2.4892012548262548 | 2.426824047458871 | 1.5904527117884357 | 1.6107795598657217 |***** DONE Capture agilent légment meilleur que celui fourni par GIAB (padding ?)CLOSED: [2023-04-14 Fri 09:48]GIAB:vcf evalThreshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure----------------------------------------------------------------------------------------------------5.000 57443 57032 984 6557 0.9830 0.8975 0.9383None 57457 57046 1009 6543 0.9826 0.8978 0.9383Happy| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio ||-------+--------+-------------+----------+----------+-------------+----------+-----------+-------+-------+---------------+------------------+----------------+-----------------+------------------------+------------------------+---------------------------+---------------------------|| INDEL | ALL | 6150 | 5007 | 1143 | 6978 | 556 | 1346 | 151 | 168 | 0.814146 | 0.901278 | 0.192892 | 0.8555 | | | 1.5434221840068787 | 1.9467178175618074 || INDEL | PASS | 6150 | 5007 | 1143 | 6978 | 556 | 1346 | 151 | 168 | 0.814146 | 0.901278 | 0.192892 | 0.8555 | | | 1.5434221840068787 | 1.9467178175618074 || SNP | ALL | 57818 | 52464 | 5354 | 56016 | 500 | 3046 | 90 | 30 | 0.907399 | 0.990561 | 0.054377 | 0.947158 | 2.4892012548262548 | 2.426824047458871 | 1.5904527117884357 | 1.6107795598657217 || SNP | PASS | 57818 | 52464 | 5354 | 56016 | 500 | 3046 | 90 | 30 | 0.907399 | 0.990561 | 0.054377 | 0.947158 | 2.4892012548262548 | 2.426824047458871 | 1.5904527117884357 | 1.6107795598657217 |AgilentThreshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure----------------------------------------------------------------------------------------------------6.000 37241 36965 449 4069 0.9880 0.9015 0.9428None 37248 36972 461 4062 0.9877 0.9017 0.9427| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio || INDEL | ALL | 2909 | 2477 | 432 | 3229 | 207 | 519 | 52 | 50 | 0.851495 | 0.923616 | 0.160731 | 0.886091 || | 1.4964850615114236 | 1.8339222614840989 || INDEL | PASS | 2909 | 2477 | 432 | 3229 | 207 | 519 | 52 | 50 | 0.851495 | 0.923616 | 0.160731 | 0.886091 | | | 1.4964850615114236 | 1.8339222614840989 || SNP | ALL | 38406 | 34793 | 3613 | 36935 | 275 | 1868 | 37 | 15 | 0.905926 | 0.992158 | 0.050575 | 0.947083 | 2.6247759222568168 | 2.5752854654538417 | 1.588953331534934 | 1.6192536889897844 || SNP | PASS | 38406 | 34793 | 3613 | 36935 | 275 | 1868 | 37 | 15 | 0.905926 | 0.992158 | 0.050575 | 0.947083 | 2.6247759222568168 | 2.5752854654538417 | 1.588953331534934 | 1.6192536889897844 |***** TODO Refaire : HiSeq4000 + agilent sureselect + génome "prêt à l'emploi"SCHEDULED: <2023-07-08 Sat>**** TODO HG003 :hg003:hg38:***** Notes#+begin_src shNXF_OPTS=-D"user.name=${USER}" nextflow run main.nf -profile standard,helios --input /Work/Groups/bisonex/data/giab/GRCh38/HG003_{1,2}.fq.gz -bg#+end_src#+begin_src shNXF_OPTS=-D"user.name=${USER}" nextflow run workflows/compareVCF.nf -profile standard,helios -resume --outdir=compareHG003 --test.id=HG003 --test.query=out/HG003_1/variantCalling/haplotypecaller/HG003_1.vcf.gz --test.compare=vcfeval,happy --test.capture=data/AgilentSureSelectv05_hg38.bed#+end_srcvcfevalThreshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure----------------------------------------------------------------------------------------------------5.000 36745 36473 486 3988 0.9869 0.9021 0.9426None 36748 36476 495 3985 0.9866 0.9022 0.9425$ zcat NA12878.snp_roc.tsv.gz | tail -n 1 | awk '{print $7 $6}'happyType Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratioINDEL ALL 2731 2290 441 3092 208 577 62 53 0.838521 0.917296 0.186611 0.876141 NaN NaN 1.505145 1.888993INDEL PASS 2731 2290 441 3092 208 577 62 53 0.838521 0.917296 0.186611 0.876141 NaN NaN 1.505145 1.888993SNP ALL 37997 34481 3516 36861 306 2074 33 13 0.907466 0.991204 0.056265 0.947488 2.611269 2.565915 1.555780 1.621727SNP PASS 37997 34481 3516 36861 306 2074 33 13 0.907466 0.991204 0.056265 0.947488 2.611269 2.5659***** TODO Refaire : HiSeq4000 + agilent sureselect + génome "prêt à l'emploi"SCHEDULED: <2023-07-08 Sat>**** TODO HG004 :hg38:hg004:#+begin_src shNXF_OPTS=-D"user.name=${USER}" nextflow run main.nf -profile standard,helios --input /Work/Groups/bisonex/data/giab/GRCh38/HG004_{1,2}.fq.gz -bg#+end_srcvcfevalThreshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure----------------------------------------------------------------------------------------------------6.000 36938 36678 421 4040 0.9887 0.9014 0.9430None 36942 36682 432 4036 0.9884 0.9015 0.9429happyType Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratioINDEL ALL 2787 2388 399 3183 195 580 53 38 0.856835 0.925086 0.182218 0.889654 NaN NaN 1.507834 1.848649INDEL PASS 2787 2388 399 3183 195 580 53 38 0.856835 0.925086 0.182218 0.889654 NaN NaN 1.507834 1.848649SNP ALL 38185 34560 3625 36921 254 2107 46 7 0.905067 0.992704 0.057068 0.946862 2.589175 2.553546 1.632595 1.653534SNP PASS 38185 34560 3625 36921 254 2107 46 7 0.905067 0.992704 0.057068 0.946862 2.589175 2.553546 1.632595 1.653534***** TODO Refaire : HiSeq4000 + agilent sureselect + génome "prêt à l'emploi"SCHEDULED: <2023-07-08 Sat>**** STRT HG001 :hg001:T2T:SCHEDULED: <2023-07-03 Mon>Avec liftover : 10x moins de variants...Type,Filter,TRUTH.TOTAL,TRUTH.TP,TRUTH.FN,QUERY.TOTAL,QUERY.FP,QUERY.UNK,FP.gt,FP.al,METRIC.Recall,METRIC.Precision,METRIC.Frac_NA,METRIC.F1_Score,TRUTH.TOTAL.TiTv_ratio,QUERY.TOTAL.TiTv_ratio,TRUTH.TOTAL.het_hom_ratio,QUERY.TOTAL.het_hom_ratioINDEL,ALL,413,246,167,751,289,215,2,93,0.595642,0.460821,0.286285,0.519629,,,2.4285714285714284,2.4651162790697674INDEL,PASS,413,246,167,751,289,215,2,93,0.595642,0.460821,0.286285,0.519629,,,2.4285714285714284,2.4651162790697674SNP,ALL,11236,10985,251,23597,9771,2841,26,58,0.977661,0.529245,0.120397,0.686734,3.1146100329549617,2.857049501715406,3.640644361833953,2.1146328578975173SNP,PASS,11236,10985,251,23597,9771,2841,26,58,0.977661,0.529245,0.120397,0.686734,3.1146100329549617,2.857049501715406,3.640644361833953,2.1146328578975173**** TODO HG002 :hg002:T2T:SCHEDULED: <2023-07-07 Fri>**** TODO HG003 :hg003:T2T:SCHEDULED: <2023-07-07 Fri>**** TODO HG004 :hg004:T2T:SCHEDULED: <2023-07-07 Fri>**** TODO Résumer résultats pour Paul + article :resultats:hg38:SCHEDULED: <2023-07-10 Mon>Refaire résultats**** TODO Plot : ashkenazim trio :hg38:SCHEDULED: <2023-07-10 Mon>/Entered on/ [2023-04-16 Sun 17:29]Refaire résultats*** KILL Platinum genomeCLOSED: [2023-06-14 Wed 22:37]https://emea.illumina.com/platinumgenomes.html*** TODO Séquencer NA12878Discussion avec Paul : sous-traitant ne nous donnera pas les données, il faut commander l'ADN**** DONE ADN commandéCLOSED: [2023-06-30 Fri 22:29]** TODO Insilico :centogene:*** TODO tous les variants centogène**** DONE Extraire liste des SNVsCLOSED: [2023-04-22 Sat 17:32] SCHEDULED: <2023-04-17 Mon>***** DONE Corriger manquant à la mainCLOSED: [2023-04-22 Sat 17:31]La sortie est sauvegardé dans git-annex : variants_success.csv***** DONE AutomatiqueCLOSED: [2023-04-22 Sat 17:31]**** DONE Convert SNVs : transcript -> génomiqueCLOSED: [2023-06-03 Sat 17:16]***** DONE Variant_recoderCLOSED: [2023-04-26 Wed 21:21] SCHEDULED: <2023-04-22 Sat>****** KILL Haskell: 160 manquant : recoded-success.csvCLOSED: [2023-04-25 Tue 18:32]La liste des variants a été générée en Haskel l et nettoyée à la main.On générer une liste de variant pour variant_rec oder et on soumet tout d'un coup.[[file:~/recherche/bisonex/parsevariants/app/Main.hs][parsevariant]]#+begin_src haskellrecodeVariant = doprepareVariantRecod er "variant_success.csv" "renamed.csv"runVariantRecoder "renamed.csv" "recoded.json"#+end_src#+RESULTS:: <interactive>:4:3-19: error:: Variable not in scope: runVariantRecoder :: String -> String -> t: ghProblème : 160 n'ont pas pu être lu sur 820, probablement à cause du numéro mineur de transcritLa sortie est sauvegardé dans git-annex : variants-recoded-raw.json.****** KILL JuliaCLOSED: [2023-04-25 Tue 18:32]On regénère la liste de variant et on passe à Julia pour préparer l'appel en parallèle à variant recoder[[file:~/recherche/bisonex/parsevariants/variantRecoder.jl][variantRecoder.jl]]#+begin_src juliasetupVariantRecoder(unique(init), n)#+end_srcPuis#+begin_src shparallel -a parallel-recoder.sh --jobs 10#+end_srcOn récupère les résultats#+begin_src julia(fails, success) = mergeVariantRecoder(n)CSV.write(fSuccess, success)CSV.write(fFailures, fails)#+end_srcCertains variants ne sont pas trouvé, donc on prépare un nouveau job en enlevant les versionrs mineures des transcrits#+begin_src julia# Cleanup json and txtif isfile(fSuccess) && isfile(fFailures)foreach(rm, variantRecoderInput())foreach(rm, variantRecoderOutput())endredoFails(fFailures)#+end_srcPuis#+begin_src shparallel -a parallel-recoder.sh --jobs 3#+end_srcIl manque encore 70 transcrits***** DONE Julia avec mobidetails: recode-failures-mobidetails.csvCLOSED: [2023-04-25 Tue 18:58]Nouvelle stratégie : on essaie une fois variant recoder.Pour tous les échecs, on utilise mobidetails (~170).Si l'ID n'est pas trouvé, on incrémente le numéro de version 2 fois***** DONE Reste une dizaine à corriger à la mainCLOSED: [2023-04-26 Wed 21:21]- [X] certains transcrits ont juste été supprimé- [X] Erreur de parsing, manque souvent un -#+begin_src julialastTryMobidetails("recoded-failures-mobidetails.csv")#+end_src***** DONE Fusionner donnéesCLOSED: [2023-04-26 Wed 22:35]#+begin_src juliafunction mergeAllGenomic()dNew = mergeAll("recoded-success.csv","recoded-failures-mobidetails.csv","recoded-failures-mobidetails-redo.csv")dInit = @chain DataFrame(CSV.File("variant_success.csv")) begin@transform :transcript = :transcript .* ":" .* :coding .* :codingPos .* :codingChange@select :file :transcript :classification :zygosity@rename :classificationCentogene = :classificationenddTmp = outerjoin(dInit, dNew, on = :transcript)CSV.write("variant_genomic.csv", dTmp)endfSuccess = "recoded-success.csv"fFailures = "recoded-failures.csv"# variantRecoder(fSuccess, fFailures)# mobidetailsOnFailures(fFailures)# lastTryMobidetails("recoded-failures-mobidetails.csv")mergeAllGenomic()#+end_src***** DONE Formatter donner pour simuscopCLOSED: [2023-04-28 Fri 11:55] SCHEDULE
ld | True-pos-baseline | True-pos-call | False-pos | False-neg | Precision | Sensitivity | F-measure ||-----------+-------------------+---------------+-----------+-----------+-----------+-------------+-----------|| 3.000 | 42789 | 42416 | 2598 | 8080 | 0.9423 | 0.8412 | 0.8889 || None | 42798 | 42425 | 2616 | 8071 | 0.9419 | 0.8413 | 0.8888 |Indel avec le plus petit seuil : zcat NA12878.non_snp_roc.tsv.gzAttention à inverser precision et recall !zcat NA12878.non_snp_roc.tsv.gz | tail -n 1 | awk '{print $7 $6}'0.71390.7136SNP avec le plus petit seuil : zcat NA12878.non_snp_roc.tsv.gzAttention à inverser precision et recall !$ zcat NA12878.snp_roc.tsv.gz | tail -n 1 | awk '{print $7 $6}'0.85470.9727compareNA12878-giab/vcfeval/NA12878.summary.txt| Threshold | True-pos-baseline | True-pos-call | False-pos | False-neg | Precision | Sensitivity | F-measure || 1.000 | 44812 | 44812 | 2878 | 6057 | 0.9397 | 0.8809 | 0.9093 || None | 44813 | 44813 | 2882 | 6056 | 0.9396 | 0.8809 | 0.9093 |SNP:$ zcat NA12878.snp_roc.tsv.gz | tail -n 1 | awk '{print $7 $6}'0.89370.9621indel$ zcat NA12878.non_snp_roc.tsv.gz | tail -n 1 | awk '{print $7 $6}'0.75980.7445compareNA12878-giab/happy/NA12878.summary.csv| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio ||-------+--------+-------------+----------+----------+-------------+----------+-----------+-------+-------+---------------+------------------+----------------+-----------------+------------------------+------------------------+---------------------------+---------------------------|| INDEL | ALL | 4871 | 3678 | 1193 | 7036 | 1299 | 2011 | 208 | 217 | 0.755081 | 0.741493 | 0.285816 | 0.748225 | | | 1.6174985978687606 | 2.5240506329113925 || INDEL | PASS | 4871 | 3678 | 1193 | 7036 | 1299 | 2011 | 208 | 217 | 0.755081 | 0.741493 | 0.285816 | 0.748225 | | | 1.6174985978687606 | 2.5240506329113925 || SNP | ALL | 46032 | 41138 | 4894 | 47694 | 1622 | 4930 | 362 | 31 | 0.893683 | 0.962071 | 0.103367 | 0.926617 | 2.529551552318896 | 2.4124463519313304 | 1.6206857273037931 | 1.6888675840288743 || SNP | PASS | 46032 | 41138 | 4894 | 47694 | 1622 | 4930 | 362 | 31 | 0.893683 | 0.962071 | 0.103367 | 0.926617 | 2.529551552318896 | 2.4124463519313304 | 1.6206857273037931 | 1.688867584028874 |***** KILL Résultats sans trimmingCLOSED: [2023-06-25 Sun 15:53] SCHEDULED: <2023-06-26 Mon>***** DONE Refaire : HiSeq4000 + agilent sureselect + génome "prêt à l'emploi"CLOSED: [2023-06-30 Fri 22:08] SCHEDULED: <2023-06-25 Sun>#+begin_srcnextflow run workflows/compareVCF.nf -profile standard,helios --outdir=out/HG001-SRX11061486_SRR14724513-GRCh38 --query=out/HG001-SRX11061486_SRR14724513-GRCh38/callVariant/haplotypecaller/HG001-SRX11061486_SRR14724513-GRCh38.vcf.gz --compare=vcfeval,happy -lib lib --capture=capture/Agilent_SureSelect_All_Exons_v7_hg38_Regions.bed --id=HG001#+end_srcMeilleurs résultats !| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio || INDEL | ALL | 549 | 489 | 60 | 899 | 64 | 340 | 8 | 17 | 0.89071 | 0.88551 | 0.378198 | 0.888102 | | | 1.86096256684492 | 2.247272727272727 || INDEL | PASS | 549 | 489 | 60 | 899 | 64 | 340 | 8 | 17 | 0.89071 | 0.88551 | 0.378198 | 0.888102 | | | 1.86096256684492 | 2.247272727272727 || SNP | ALL | 21973 | 21462 | 511 | 26285 | 563 | 4263 | 68 | 16 | 0.976744 | 0.974435 | 0.162184 | 0.975588 | 3.007110300820419 | 2.78468624064479 | 1.5918102430965306 | 1.8161449399656946 || SNP | PASS | 21973 | 21462 | 511 | 26285 | 563 | 4263 | 68 | 16 | 0.976744 | 0.974435 | 0.162184 | 0.975588 | 3.007110300820419 | 2.78468624064479 | 1.5918102430965306 | 1.8161449399656946 |***** KILL Utiliser d'autres données brutes ?CLOSED: [2023-06-25 Sun 15:58]https://zenodo.org/record/3597727Capture en hg37 également. Serait intéressant mais pas le temps..***** KILL Comparer avec UCSCS liftoverCLOSED: [2023-06-26 Mon 19:02] SCHEDULED: <2023-06-25 Sun>Picard liftoverinterval est basé sur UCSCSMais on n'aurait pas la différence pour NA12878 qu'on voit...**** TODO HG002 :hg002:hg38:SCHEDULED: <2023-07-14 Fri>#+begin_srcNXF_OPTS=-D"user.name=${USER}" nextflow run workflows/giabFastq.nf -profile standard,heliosNXF_OPTS=-D"user.name=${USER}" nextflow run main.nf -profile standard,helios -resume --input="/Work/Groups/bisonex/data/giab/GRCh38/HG002_{1,2}.fq.gz --test.id=HG002Only the capture file differs. Results are better using the capture file given by Agilent, stored in data/NXF_OPTS=-D"user.name=${USER}" nextflow run workflows/compareVCF.nf -profile standard,helios -resume --outdir=compareHG002 --test.id=HG002 --test.query=out/HG002_1/variantCalling/haplotypecaller/HG002_1.vcf.gz --test.compare=vcfeval,happy --test.capture=data/AgilentSureSelectv05_hg38.bed##+end_src***** DONE Mauvais résultatsCLOSED: [2023-04-14 Fri 09:42]avec vcfevalThreshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure----------------------------------------------------------------------------------------------------0.000 24585 24390 10060 39415 0.7080 0.3841 0.4980None 24585 24390 10060 39415 0.7080 0.3841 0.4980La sortie du variantCalling est celle d'happy ???On relance...***** DONE Vérifier vcf en hg38CLOSED: [2023-04-12 Wed 10:33] SCHEDULED: <2023-04-12 Wed>***** KILL Capture en hg19 ?CLOSED: [2023-04-13 Thu 09:46] SCHEDULED: <2023-04-12 Wed>***** KILL Vraiment fichier de capture ou zone d'intérêt ?CLOSED: [2023-04-13 Thu 09:45] SCHEDULED: <2023-04-12 Wed>"target region" +/- 50bp[[https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/analysis/OsloUniversityHospital_Exome_GATK_jointVC_11242015/README.txt][README]]list file describing the variant calling regions (target regions extended with 50 bp on each end)***** DONE .bed fourni par AGilent: sensbilité très mauvaiseCLOSED: [2023-04-13 Thu 09:46] SCHEDULED: <2023-04-13 Thu>Agilent SureSelect Human All Exon V5 kitDisponible en hg38Threshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure----------------------------------------------------------------------------------------------------0.000 19653 19501 6410 21657 0.7526 0.4757 0.5830None 19653 19501 6410 21657 0.7526 0.4757 0.5830***** DONE Trier par nom avec samtools sort : bons résultatsCLOSED: [2023-04-14 Fri 09:25] SCHEDULED: <2023-04-13 Thu>Avec capture fourni par GIABvcf evalThreshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure----------------------------------------------------------------------------------------------------5.000 57443 57032 984 6557 0.9830 0.8975 0.9383None 57457 57046 1009 6543 0.9826 0.8978 0.9383Happy| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio ||-------+--------+-------------+----------+----------+-------------+----------+-----------+-------+-------+---------------+------------------+----------------+-----------------+------------------------+------------------------+---------------------------+---------------------------|| INDEL | ALL | 6150 | 5007 | 1143 | 6978 | 556 | 1346 | 151 | 168 | 0.814146 | 0.901278 | 0.192892 | 0.8555 | | | 1.5434221840068787 | 1.9467178175618074 || INDEL | PASS | 6150 | 5007 | 1143 | 6978 | 556 | 1346 | 151 | 168 | 0.814146 | 0.901278 | 0.192892 | 0.8555 | | | 1.5434221840068787 | 1.9467178175618074 || SNP | ALL | 57818 | 52464 | 5354 | 56016 | 500 | 3046 | 90 | 30 | 0.907399 | 0.990561 | 0.054377 | 0.947158 | 2.4892012548262548 | 2.426824047458871 | 1.5904527117884357 | 1.6107795598657217 || SNP | PASS | 57818 | 52464 | 5354 | 56016 | 500 | 3046 | 90 | 30 | 0.907399 | 0.990561 | 0.054377 | 0.947158 | 2.4892012548262548 | 2.426824047458871 | 1.5904527117884357 | 1.6107795598657217 |***** DONE Capture agilent légment meilleur que celui fourni par GIAB (padding ?)CLOSED: [2023-04-14 Fri 09:48]GIAB:vcf evalThreshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure----------------------------------------------------------------------------------------------------5.000 57443 57032 984 6557 0.9830 0.8975 0.9383None 57457 57046 1009 6543 0.9826 0.8978 0.9383Happy| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio ||-------+--------+-------------+----------+----------+-------------+----------+-----------+-------+-------+---------------+------------------+----------------+-----------------+------------------------+------------------------+---------------------------+---------------------------|| INDEL | ALL | 6150 | 5007 | 1143 | 6978 | 556 | 1346 | 151 | 168 | 0.814146 | 0.901278 | 0.192892 | 0.8555 | | | 1.5434221840068787 | 1.9467178175618074 || INDEL | PASS | 6150 | 5007 | 1143 | 6978 | 556 | 1346 | 151 | 168 | 0.814146 | 0.901278 | 0.192892 | 0.8555 | | | 1.5434221840068787 | 1.9467178175618074 || SNP | ALL | 57818 | 52464 | 5354 | 56016 | 500 | 3046 | 90 | 30 | 0.907399 | 0.990561 | 0.054377 | 0.947158 | 2.4892012548262548 | 2.426824047458871 | 1.5904527117884357 | 1.6107795598657217 || SNP | PASS | 57818 | 52464 | 5354 | 56016 | 500 | 3046 | 90 | 30 | 0.907399 | 0.990561 | 0.054377 | 0.947158 | 2.4892012548262548 | 2.426824047458871 | 1.5904527117884357 | 1.6107795598657217 |AgilentThreshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure----------------------------------------------------------------------------------------------------6.000 37241 36965 449 4069 0.9880 0.9015 0.9428None 37248 36972 461 4062 0.9877 0.9017 0.9427| Type | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio || INDEL | ALL | 2909 | 2477 | 432 | 3229 | 207 | 519 | 52 | 50 | 0.851495 | 0.923616 | 0.160731 | 0.886091 | | | 1.4964850615114236 | 1.8339222614840989 || INDEL | PASS | 2909 | 2477 | 432 | 3229 | 207 | 519 | 52 | 50 | 0.851495 | 0.923616 | 0.160731 | 0.886091 | | | 1.4964850615114236 | 1.8339222614840989 || SNP | ALL | 38406 | 34793 | 3613 | 36935 | 275 | 1868 | 37 | 15 | 0.905926 | 0.992158 | 0.050575 | 0.947083 | 2.6247759222568168 | 2.5752854654538417 | 1.588953331534934 | 1.6192536889897844 || SNP | PASS | 38406 | 34793 | 3613 | 36935 | 275 | 1868 | 37 | 15 | 0.905926 | 0.992158 | 0.050575 | 0.947083 | 2.6247759222568168 | 2.5752854654538417 | 1.588953331534934 | 1.6192536889897844 |***** TODO Refaire : HiSeq4000 + agilent sureselect + génome "prêt à l'emploi"SCHEDULED: <2023-07-12 Wed>**** TODO HG003 :hg003:hg38:***** Notes#+begin_src shNXF_OPTS=-D"user.name=${USER}" nextflow run main.nf -profile standard,helios --input /Work/Groups/bisonex/data/giab/GRCh38/HG003_{1,2}.fq.gz -bg#+end_src#+begin_src shNXF_OPTS=-D"user.name=${USER}" nextflow run workflows/compareVCF.nf -profile standard,helios -resume --outdir=compareHG003 --test.id=HG003 --test.query=out/HG003_1/variantCalling/haplotypecaller/HG003_1.vcf.gz --test.compare=vcfeval,happy --test.capture=data/AgilentSureSelectv05_hg38.bed#+end_srcvcfevalThreshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure----------------------------------------------------------------------------------------------------5.000 36745 36473 486 3988 0.9869 0.9021 0.9426None 36748 36476 495 3985 0.9866 0.9022 0.9425$ zcat NA12878.snp_roc.tsv.gz | tail -n 1 | awk '{print $7 $6}'happyType Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratioINDEL ALL 2731 2290 441 3092 208 577 62 53 0.838521 0.917296 0.186611 0.876141 NaN NaN 1.505145 1.888993INDEL PASS 2731 2290 441 3092 208 577 62 53 0.838521 0.917296 0.186611 0.876141 NaN NaN 1.505145 1.888993SNP ALL 37997 34481 3516 36861 306 2074 33 13 0.907466 0.991204 0.056265 0.947488 2.611269 2.565915 1.555780 1.621727SNP PASS 37997 34481 3516 36861 306 2074 33 13 0.907466 0.991204 0.056265 0.947488 2.611269 2.5659***** TODO Refaire : HiSeq4000 + agilent sureselect + génome "prêt à l'emploi"SCHEDULED: <2023-07-14 Fri>**** TODO HG004 :hg38:hg004:#+begin_src shNXF_OPTS=-D"user.name=${USER}" nextflow run main.nf -profile standard,helios --input /Work/Groups/bisonex/data/giab/GRCh38/HG004_{1,2}.fq.gz -bg#+end_srcvcfevalThreshold True-pos-baseline True-pos-call False-pos False-neg Precision Sensitivity F-measure----------------------------------------------------------------------------------------------------6.000 36938 36678 421 4040 0.9887 0.9014 0.9430None 36942 36682 432 4036 0.9884 0.9015 0.9429happyType Filter TRUTH.TOTAL TRUTH.TP TRUTH.FN QUERY.TOTAL QUERY.FP QUERY.UNK FP.gt FP.al METRIC.Recall METRIC.Precision METRIC.Frac_NA METRIC.F1_Score TRUTH.TOTAL.TiTv_ratio QUERY.TOTAL.TiTv_ratio TRUTH.TOTAL.het_hom_ratio QUERY.TOTAL.het_hom_ratioINDEL ALL 2787 2388 399 3183 195 580 53 38 0.856835 0.925086 0.182218 0.889654 NaN NaN 1.507834 1.848649INDEL PASS 2787 2388 399 3183 195 580 53 38 0.856835 0.925086 0.182218 0.889654 NaN NaN 1.507834 1.848649SNP ALL 38185 34560 3625 36921 254 2107 46 7 0.905067 0.992704 0.057068 0.946862 2.589175 2.553546 1.632595 1.653534SNP PASS 38185 34560 3625 36921 254 2107 46 7 0.905067 0.992704 0.057068 0.946862 2.589175 2.553546 1.632595 1.653534***** TODO Refaire : HiSeq4000 + agilent sureselect + génome "prêt à l'emploi"SCHEDULED: <2023-07-14 Fri>**** STRT HG001 :hg001:T2T:SCHEDULED: <2023-07-03 Mon>Avec liftover : 10x moins de variants...Type,Filter,TRUTH.TOTAL,TRUTH.TP,TRUTH.FN,QUERY.TOTAL,QUERY.FP,QUERY.UNK,FP.gt,FP.al,METRIC.Recall,METRIC.Precision,METRIC.Frac_NA,METRIC.F1_Score,TRUTH.TOTAL.TiTv_ratio,QUERY.TOTAL.TiTv_ratio,TRUTH.TOTAL.het_hom_ratio,QUERY.TOTAL.het_hom_ratioINDEL,ALL,413,246,167,751,289,215,2,93,0.595642,0.460821,0.286285,0.519629,,,2.4285714285714284,2.4651162790697674INDEL,PASS,413,246,167,751,289,215,2,93,0.595642,0.460821,0.286285,0.519629,,,2.4285714285714284,2.4651162790697674SNP,ALL,11236,10985,251,23597,9771,2841,26,58,0.977661,0.529245,0.120397,0.686734,3.1146100329549617,2.857049501715406,3.640644361833953,2.1146328578975173SNP,PASS,11236,10985,251,23597,9771,2841,26,58,0.977661,0.529245,0.120397,0.686734,3.1146100329549617,2.857049501715406,3.640644361833953,2.1146328578975173**** TODO HG002 :hg002:T2T:**** TODO HG003 :hg003:T2T:**** TODO HG004 :hg004:T2T:**** TODO Résumer résultats pour Paul + article :resultats:hg38:SCHEDULED: <2023-07-10 Mon>Refaire résultats**** TODO Plot : ashkenazim trio :hg38:SCHEDULED: <2023-07-10 Mon>/Entered on/ [2023-04-16 Sun 17:29]Refaire résultats*** KILL Platinum genomeCLOSED: [2023-06-14 Wed 22:37]https://emea.illumina.com/platinumgenomes.html*** TODO Séquencer NA12878Discussion avec Paul : sous-traitant ne nous donnera pas les données, il faut commander l'ADN**** DONE ADN commandéCLOSED: [2023-06-30 Fri 22:29]** TODO Insilico :centogene:*** TODO tous les variants centogène**** DONE Extraire liste des SNVsCLOSED: [2023-04-22 Sat 17:32] SCHEDULED: <2023-04-17 Mon>***** DONE Corriger manquant à la mainCLOSED: [2023-04-22 Sat 17:31]La sortie est sauvegardé dans git-annex : variants_success.csv***** DONE AutomatiqueCLOSED: [2023-04-22 Sat 17:31]**** DONE Convert SNVs : transcript -> génomiqueCLOSED: [2023-06-03 Sat 17:16]***** DONE Variant_recoderCLOSED: [2023-04-26 Wed 21:21] SCHEDULED: <2023-04-22 Sat>****** KILL Haskell: 160 manquant : recoded-success.csvCLOSED: [2023-04-25 Tue 18:32]La liste des variants a été générée en Haskel l et nettoyée à la main.On générer une liste de variant pour variant_rec oder et on soumet tout d'un coup.[[file:~/recherche/bisonex/parsevariants/app/Main.hs][parsevariant]]#+begin_src haskellrecodeVariant = doprepareVariantRecod er "variant_success.csv" "renamed.csv"runVariantRecoder "renamed.csv" "recoded.json"#+end_src#+RESULTS:: <interactive>:4:3-19: error:: Variable not in scope: runVariantRecoder :: String -> String -> t: ghProblème : 160 n'ont pas pu être lu sur 820, probablement à cause du numéro mineur de transcritLa sortie est sauvegardé dans git-annex : variants-recoded-raw.json.****** KILL JuliaCLOSED: [2023-04-25 Tue 18:32]On regénère la liste de variant et on passe à Julia pour préparer l'appel en parallèle à variant recoder[[file:~/recherche/bisonex/parsevariants/variantRecoder.jl][variantRecoder.jl]]#+begin_src juliasetupVariantRecoder(unique(init), n)#+end_srcPuis#+begin_src shparallel -a parallel-recoder.sh --jobs 10#+end_srcOn récupère les résultats#+begin_src julia(fails, success) = mergeVariantRecoder(n)CSV.write(fSuccess, success)CSV.write(fFailures, fails)#+end_srcCertains variants ne sont pas trouvé, donc on prépare un nouveau job en enlevant les versionrs mineures des transcrits#+begin_src julia# Cleanup json and txtif isfile(fSuccess) && isfile(fFailures)foreach(rm, variantRecoderInput())foreach(rm, variantRecoderOutput())endredoFails(fFailures)#+end_srcPuis#+begin_src shparallel -a parallel-recoder.sh --jobs 3#+end_srcIl manque encore 70 transcrits***** DONE Julia avec mobidetails: recode-failures-mobidetails.csvCLOSED: [2023-04-25 Tue 18:58]Nouvelle stratégie : on essaie une fois variant recoder.Pour tous les échecs, on utilise mobidetails (~170).Si l'ID n'est pas trouvé, on incrémente le numéro de version 2 fois***** DONE Reste une dizaine à corriger à la mainCLOSED: [2023-04-26 Wed 21:21]- [X] certains transcrits ont juste été supprimé- [X] Erreur de parsing, manque souvent un -#+begin_src julialastTryMobidetails("recoded-failures-mobidetails.csv")#+end_src***** DONE Fusionner donnéesCLOSED: [2023-04-26 Wed 22:35]#+begin_src juliafunction mergeAllGenomic()dNew = mergeAll("recoded-success.csv","recoded-failures-mobidetails.csv","recoded-failures-mobidetails-redo.csv")dInit = @chain DataFrame(CSV.File("variant_success.csv")) begin@transform :transcript = :transcript .* ":" .* :coding .* :codingPos .* :codingChange@select :file :transcript :classification :zygosity@rename :classificationCentogene = :classificationenddTmp = outerjoin(dInit, dNew, on = :transcript)CSV.write("variant_genomic.csv", dTmp)endfSuccess = "recoded-success.csv"fFailures = "recoded-failures.csv"# variantRecoder(fSuccess, fFailures)# mobidetailsOnFailures(fFailures)# lastTryMobidetails("recoded-failures-mobidetails.csv")mergeAllGenomic()#+end_src***** DONE Formatter donner pour simuscopCLOSED: [2023-04-28 Fri 11:55] SCHEDULE
- 74342974 74343101 128browser details YourSeq 23 104 128 128 96.0% chr19 + 33396097 33396121 25******** DONE Bwa mem à la main GRCh38.p13 : on est dans une zone NWCLOSED: [2023-06-04 Sun 21:51]On met les 2 reads dans des fichiers séparés puis#+begin_src shcd /Work/Users/apraga/bisonex/tests/xamscissors/alignbwa mem /Work/Groups/bisonex/data/genome/GRCh38.p13/bwa/genomeRef test1.fq test2.fq#+end_srcA00853:477:HMLWYDSX3:2:2444:22354:28870 97 NW_021160016.1 172243 0 128M = 172243 128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTTGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFF,FFFFFF,FFFFFFFFFFFF:FF::FF NM:i:2 MD:Z:22A30C7MC:Z:128M AS:i:118 XS:i:118 XA:Z:NC_000015.10,+74342974,128M,2;A00853:477:HMLWYDSX3:2:2444:22354:28870 145 NW_021160016.1 172243 0 128M = 172243 -128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTCGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFF:FFFFFF,FFF:,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFF:FF NM:i:1 MD:Z:22A105 MC:Z:128M AS:i:123 XS:i:123 XA:Z:NC_000015.10,-74342974,128M,1;******** DONE GRCh38.p14: idemCLOSED: [2023-06-04 Sun 21:51]A00853:477:HMLWYDSX3:2:2444:22354:28870 97 NW_021160016.1 172243 0 128M = 172243 128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTTGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFF,FFFFFF,FFFFFFFFFFFF:FF::FF NM:i:2 MD:Z:22A30C7MC:Z:128M AS:i:118 XS:i:118 XA:Z:NC_000015.10,+74342974,128M,2;A00853:477:HMLWYDSX3:2:2444:22354:28870 145 NW_021160016.1 172243 0 128M = 172243 -128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTCGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFF:FFFFFF,FFF:,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFF:FF NM:i:1 MD:Z:22A105 MC:Z:128M AS:i:123 XS:i:123 XA:Z:NC_000015.10,-74342974,128M,1;******** DONE GRCh38 : okCLOSED: [2023-06-04 Sun 22:15]bwa mem /Work/Projects/bisonex/data/genome/GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna test1.fq test2.fq******* DONE Vérifier que les reads ont la même qualité sur les fichiers d'origine: ouiCLOSED: [2023-06-04 Sun 21:07]******* DONE Supprimer les NW_ ?CLOSED: [2023-06-10 Sat 10:40] SCHEDULED: <2023-06-04 Sun>@A00853:477:HMLWYDSX3:3:2114:14742:8860CAGGCCAGCCGCTCAGCCCGCTCCTTTCACCCTCTGCAGGAGAGCCTCGTGGCAGGCCAGTGGAGGGACATGATGGACTACATGCTCCAAGGGGTGGCGCAGCCGAGCATGGAAGAGGGCTCTGGACAGCTCCTGGAAGGGCACTTGCAC+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF@A00853:477:HMLWYDSX3:3:2114:14742:8860CTTTTGCTTGTCCCCAGGACGCACCTCAGGGTGGTGAAGCAAAAAAACCACGGCCCAGGAGAGGGTGGGTGCTGTGGTCTCAGTGCCACCGATCAGGAGGTCCACTGCAGCCATGTGCAAGTGCCCTTCCAGGAGCTGTCCAGAGCCCTCT+FFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFF,FFFFFFFFFFFF:F:FFFF:FFFFF,,FFF:FFFFFFFFFF,FFFFFFF,FFFFFFFFFFF,FFFFFFFFF:FFFF,F:FFFFF:FFFFFFFFF:FFFF,FFFFFFFFF******* DONE Supprimer NW_ et NT_***** TODO Phase 2 : chr22, vaf variable :T2T:SCHEDULED: <2023-07-10 Mon>****** TODO Phase 3 : tous SNV, vaf variable :T2T:SCHEDULED: <2023-07-07 Fri>***** TODO Test Indel**** Divers***** DONE Vérifier nombre de reads fastq - bamCLOSED: [2022-10-09 Sun 22:31]*** KILL Liste varants "clinically relevent" (Clinge - CT-R d)CLOSED: [2023-06-25 Sun 15:53] SCHEDULED: <2023-06-25 Sun>[cite:@wilcox2021]Vu avec alexis: pas notre cas d'usage
- 74342974 74343101 128browser details YourSeq 23 104 128 128 96.0% chr19 + 33396097 33396121 25******** DONE Bwa mem à la main GRCh38.p13 : on est dans une zone NWCLOSED: [2023-06-04 Sun 21:51]On met les 2 reads dans des fichiers séparés puis#+begin_src shcd /Work/Users/apraga/bisonex/tests/xamscissors/alignbwa mem /Work/Groups/bisonex/data/genome/GRCh38.p13/bwa/genomeRef test1.fq test2.fq#+end_srcA00853:477:HMLWYDSX3:2:2444:22354:28870 97 NW_021160016.1 172243 0 128M = 172243 128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTTGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFF,FFFFFF,FFFFFFFFFFFF:FF::FF NM:i:2 MD:Z:22A30C7MC:Z:128M AS:i:118 XS:i:118 XA:Z:NC_000015.10,+74342974,128M,2;A00853:477:HMLWYDSX3:2:2444:22354:28870 145 NW_021160016.1 172243 0 128M = 172243 -128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTCGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFF:FFFFFF,FFF:,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFF:FF NM:i:1 MD:Z:22A105 MC:Z:128M AS:i:123 XS:i:123 XA:Z:NC_000015.10,-74342974,128M,1;******** DONE GRCh38.p14: idemCLOSED: [2023-06-04 Sun 21:51]A00853:477:HMLWYDSX3:2:2444:22354:28870 97 NW_021160016.1 172243 0 128M = 172243 128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTTGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFF,FFFFFF,FFFFFFFFFFFF:FF::FF NM:i:2 MD:Z:22A30C7MC:Z:128M AS:i:118 XS:i:118 XA:Z:NC_000015.10,+74342974,128M,2;A00853:477:HMLWYDSX3:2:2444:22354:28870 145 NW_021160016.1 172243 0 128M = 172243 -128 CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTCGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC FFFFFFFFFFFFF:FFFFFF,FFF:,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFF:FF NM:i:1 MD:Z:22A105 MC:Z:128M AS:i:123 XS:i:123 XA:Z:NC_000015.10,-74342974,128M,1;******** DONE GRCh38 : okCLOSED: [2023-06-04 Sun 22:15]bwa mem /Work/Projects/bisonex/data/genome/GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna test1.fq test2.fq******* DONE Vérifier que les reads ont la même qualité sur les fichiers d'origine: ouiCLOSED: [2023-06-04 Sun 21:07]******* DONE Supprimer les NW_ ?CLOSED: [2023-06-10 Sat 10:40] SCHEDULED: <2023-06-04 Sun>@A00853:477:HMLWYDSX3:3:2114:14742:8860CAGGCCAGCCGCTCAGCCCGCTCCTTTCACCCTCTGCAGGAGAGCCTCGTGGCAGGCCAGTGGAGGGACATGATGGACTACATGCTCCAAGGGGTGGCGCAGCCGAGCATGGAAGAGGGCTCTGGACAGCTCCTGGAAGGGCACTTGCAC+FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF@A00853:477:HMLWYDSX3:3:2114:14742:8860CTTTTGCTTGTCCCCAGGACGCACCTCAGGGTGGTGAAGCAAAAAAACCACGGCCCAGGAGAGGGTGGGTGCTGTGGTCTCAGTGCCACCGATCAGGAGGTCCACTGCAGCCATGTGCAAGTGCCCTTCCAGGAGCTGTCCAGAGCCCTCT+FFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFF,FFFFFFFFFFFF:F:FFFF:FFFFF,,FFF:FFFFFFFFFF,FFFFFFF,FFFFFFFFFFF,FFFFFFFFF:FFFF,F:FFFFF:FFFFFFFFF:FFFF,FFFFFFFFF******* DONE Supprimer NW_ et NT_***** TODO Phase 2 : chr22, vaf variable :T2T:SCHEDULED: <2023-07-10 Mon>****** TODO Phase 3 : tous SNV, vaf variable :T2T:SCHEDULED: <2023-07-14 Fri>***** TODO Test Indel**** Divers***** DONE Vérifier nombre de reads fastq - bamCLOSED: [2022-10-09 Sun 22:31]*** KILL Liste varants "clinically relevent" (Clinge - CT-R d)CLOSED: [2023-06-25 Sun 15:53] SCHEDULED: <2023-06-25 Sun>[cite:@wilcox2021]Vu avec alexis: pas notre cas d'usage
:ARCHIVE_CATEGORY: projects:ARCHIVE_TODO: DONE:END:* FreeBSD :freebsd::PROPERTIES::ARCHIVE_TIME: 2023-07-07 Fri 18:46:ARCHIVE_FILE: ~/roam/personal/projects.org:ARCHIVE_CATEGORY: projects:END:** KILL ormolu 0.5.0.0CLOSED: [2022-10-22 Sat 23:36] SCHEDULED: <2022-07-30 Sat>** Kitty*** KILL Problème sur fetchdirCLOSED: [2022-09-22 Thu 10:45]Commiter au courant, attente de résolution** KILL [[https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=264158][pkgconf est trop lent sur freebsd]]CLOSED: [2023-07-07 Fri 18:46]Problème persiste avec dernière version* DONE Ordure ménagèresCLOSED: [2023-06-11 Sun 21:40]:PROPERTIES::ARCHIVE_TIME: 2023-07-07 Fri 18:51:ARCHIVE_FILE: ~/roam/personal/projects.org:ARCHIVE_OLPATH: Maison
Envoyé RIB le <2023-06-11 Sun>* DONE Badge déchetterieCLOSED: [2023-07-07 Fri 18:48] SCHEDULED: <2023-07-12 Wed>:PROPERTIES::ARCHIVE_TIME: 2023-07-07 Fri 18:51:ARCHIVE_FILE: ~/roam/personal/projects.org:ARCHIVE_OLPATH: Maison:ARCHIVE_CATEGORY: projects:ARCHIVE_TODO: DONE:END:/Entered on/ [2023-07-02 Sun 11:03]* DONE Changer kit chaineCLOSED: [2023-04-01 Sat 17:24] SCHEDULED: <2023-04-01 Sat>:PROPERTIES::ARCHIVE_TIME: 2023-07-07 Fri 18:51:ARCHIVE_FILE: ~/roam/personal/projects.org:ARCHIVE_OLPATH: Moto:ARCHIVE_CATEGORY: moto:ARCHIVE_TODO: DONE:END:RV pris yamah41000km