B:BD[
17.43661] → [
14.25134:33326]
B:BD[
14.33326] → [
3.30:4885]
from summarising data in this way. "
**** DONE Mail alexis
CLOSED: [2023-08-20 Sun 13:45] SCHEDULED: <2023-08-20 Sun>
**** TODO Données simuscop 200x
SCHEDULED: <2023-10-29 Sun>
**** DONE En T2T avec liftover (filtre = spip) : ok mais lent et trop de variants :tests:
CLOSED: [2023-09-17 Sun 17:13] SCHEDULED: <2023-09-17 Sun>
1. Conversion en bed
#+begin_src sh :dir:~/code/sanger
open snvs-cento-sanger.csv | select chrom pos | insert pos2 {$in.pos } | to csv --separator="\t" | save snvs-cento-sanger.bed -f
#+end_src
2. Liftover avec UCSC (en ligne)
NB: vérifié sur le premier résultat en cherche le read contenant le variant (samtools view -r puis samtools view | grep en T2T) et avec l'aide d'IGV, on a un variant qui correspond en
chr1:10757746
3. En supposant que l'ordre des variants n'a pas changé, on ajoute simplement REF et ALT avec annotateLifted.jl
Annotation spip *très lente* : 1h13 !
Résultat:
2×3 DataFrame
Row │ variant meanQual depth
│ String Float64 Int64
─────┼──────────────────────────────────────
1 │ chr12:g.13594572 60.0 1
2 │ chr17:g.10204026 60.0 1
144 found over 146
filter depth : another 0 missed variants
filter poly : another 0 missed variants
filter vep : another 0 missed variants
Et on a trop de variants en sortie (7330 !)
**** DONE Mail Paul avec résultats filtre en T2T + nouveau schéma
CLOSED: [2023-09-17 Sun 23:15] SCHEDULED: <2023-09-17 Sun>
** TODO Medically relevant genes
SCHEDULED: <2023-11-02 Thu>
/Entered on/ [2023-10-18 Wed 22:37]
* Ré-interprétation :reanalysis:
** DONE Lancer tests sur données brutes [225/250] <(samples.csv)> <(runs.waiting)>
CLOSED: [2023-10-14 Sat 11:58] SCHEDULED: <2023-10-08 Sun>
- [X] 100222_63015289
- [X] 1600304839_63051311
- [X] 1900007827_62913191
- [X] 1900398899_62999500
- [X] 1900486799_62913197
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- [X] 2100622601_62908060
- [X] 2100622705_62908063
- [X] 2100640027_62911936
- [X] 2100645285_62913212
- [X] 2100661411_62914081
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- [X] 2100708257_62921596
- [X] 2100738732_62926501
- [X] 2100738850_62926509
- [X] 2100746751_62926505
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- [X] 2100782349_62931722
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- [X] 2100782559_62931718
- [X] 2100799204_62934768
- [X] 2200010202_62940284
- [X] 2200023600_62940631
- [X] 2200024348_62999591
- [X] 2200027505_62942457
- [X] 2200038776_62943412
- [X] 2200041919_62943405
- [X] 2200088014_62951326
- [X] 2200146652_62959388
- [X] 2200151850_62960953
- [X] 2200160014_62959475
- [X] 2200160070_62959478
- [X] 2200201368_62967471
- [X] 2200201400_62967470
- [X] 2200265558_62976332
- [X] 2200265605_62976401
- [X] 2200267046_62975192
- [X] 2200273878_62999530
- [X] 2200279708_62977002
- [X] 2200284408_62979102
- [X] 2200293987_62979116
- [X] 2200294359_62979118
- [X] 2200306299_62982217
- [X] 2200306539_62982193
- [X] 220030671_62982211
- [X] 2200307058_62982231
- [X] 2200307108_62982196
- [X] 2200307136_62982221
- [X] 2200307199_62982239
- [X] 2200307230_62982234
- [X] 2200307262_62982219
- [X] 2200307297_62982227
- [X] 2200324510_62985453
- [X] 2200324549_62985478
- [X] 2200324573_62985445
- [X] 2200324594_62985467
- [X] 2200324606_62985463
- [X] 2200324614_62985459
- [X] 2200338306_62985430
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- [X] 2200343910_62989460
- [X] 2200343938_62989451
- [X] 2200343966_62989456
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- [X] 2200344013_62989464
- [X] 2200349749_62989465
- [X] 2200363462_62988848
- [X] 2200377880_62991993
- [X] 2200378032_62991991
- [X] 2200383996_62993828
- [X] 2200384015_62993796
- [X] 2200384046_62993822
- [X] 2200384117_62993808
- [X] 2200384187_62993825
- [X] 2200384231_62992898
- [X] 2200385658_63060260
- [X] 2200394260_62994732
- [X] 2200395817_62994742
- [X] 2200396731_62994737
- [X] 2200424073_62999579
- [X] 2200424207_62999632
- [X] 2200426178_62999630
- [X] 2200426243_62999635
- [X] 2200426466_62999605
- [X] 2200426642_62999627
- [X] 2200427406_62999649
- [X] 2200427512_62999639
- [X] 2200428953_62999572
- [X] 2200428981_62999600
- [X] 2200428999_62999592
- [X] 2200441970_63000868
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- [X] 2200442135_63000864
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- [X] 2200451801_63003573
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- [X] 2200451894_63004210
- [X] 2200456165_63051294
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- [X] 2200460121_63004684
- [X] 2200467051_63003856
- [X] 2200467225_63004940
- [X] 2200467261_63004930
- [X] 2200467338_63004925
- [X] 2200470099_63004485
- [X] 2200470142_63004480
- [X] 2200471780_63004362
- [X] 2200480910_63006466
- [X] 2200495073_63010427
- [X] 2200495510_63009152
- [X] 2200508677_63060252
- [X] 2200510531_63012582
- [X] 2200510628_63012549
- [X] 2200510657_63012554
- [X] 2200511249_63012533
- [X] 2200511274_63012586
- [X] 2200517952_63060399
- [X] 2200519525_63060439
- [X] 2200524009_63014044
- [X] 2200524609_63014046
- [X] 2200524616_63014048
- [X] 2200533429_63060425
- [X] 2200539735_63060406
- [X] 2200549908_63019339
- [X] 2200549965_63019349
- [X] 2200550414_63019357
- [X] 2200550471_63020031
- [X] 2200550490_63019351
- [X] 2200550505_63019340
- [X] 2200555565_63018614
- [X] 2200559438_63020029
- [X] 2200559682_63020030
- [X] 2200559713_63019623
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- [X] 2200569969_63019991
- [X] 2200570001_63021580
- [X] 2200570025_63021490
- [X] 2200570035_63021491
- [X] 2200570042_63021493
- [X] 2200570050_63021494
- [X] 2200579897_63024910
- [X] 2200583995_63024866
- [X] 2200584035_63024905
- [X] 2200584069_63024888
- [X] 2200584126_63024810
- [X] 2200589507_63026712
- [X] 2200597365_63027994
- [X] 2200597480_63027988
- [X] 2200597752_63026853
- [X] 2200597778_63027992
- [X] 22005977_63026903
- [X] 2200609031_63026527
- [X] 2200614198_63113928
- [X] 2200620372_63030821
- [X] 2200620442_63030810
- [X] 2200620498_63030816
- [X] 2200620628_63031031
- [X] 2200622310_63030984
- [X] 2200622355_63030956
- [X] 2200625369_63028699
- [X] 2200625410_63028697
- [X] 2200625536_63028694
- [X] 2200630189_63030665
- [X] 2200635149_63033182
- [X] 2200644544_63037731
- [X] 2200644594_63037725
- [X] 2200650089_63038093
- [X] 2200666292_63076568
- [X] 2200669188_63036688
- [X] 2200669320_63040259
- [X] 2200669383_63040254
- [X] 2200669414_63040257
- [X] 2200669446_63040251
- [X] 2200680342_63105271
- [X] 2200694535_63042853
- [X] 2200694789_63042862
- [X] 2200694858_63042702
- [X] 2200694917_63042696
- [X] 2200699290_63043047
- [X] 2200699345_63040238
- [X] 2200699383_63043050
- [X] 2200699412_63040731
- [X] 220071551_63048935
- [X] 2200731515_63048963
- [X] 2200748145_63051198
- [X] 2200748171_63051213
- [X] 2200751046_63051249
- [X] 2200751101_63051234
- [X] 2200766471_63054590
- [X] 2200767731_63054595
- [X] 2200767822_63054464
- [X] 2200775505_63060410
- [X] 2200850441_63019345
- [X] 220597589_63026879
- [X] 2300003253_63060430
- [X] 2300005679_63060370
- [X] 2300009914_63060390
- [X] 2300028784_63060001
- [X] 2300036815_63063357
- [X] 2300055382_63061874
- [X] 2300055421_63061871
- [X] 2300055440_63061880
- [X] 230006894_63064950
- [X] 2300071111_63070356
- [X] 2300083434_63071675
- [X] 2300103609_63076239
- [X] 2300104572_63076232
- [X] 2300109602_63076765
- [X] 2300109665_63076770
- [X] 2300119721_63078732
- [X] 2300137773_63078133
- [X] 2300137834_63078123
- [X] 2300167821_63086183
- [X] 2300172698_63113453
- [X] 2300188216_63090609
- [X] 2300188281_63090632
- [ ] 2300188800_63090616
- [ ] 2300193193645_63090623
- [ ] 2300193668_63090611
- [ ] 2300195426_63090608
- [ ] 2300201017_63089636
- [ ] 2300227479_63098330
- [ ] 2300232688_63130821
- [ ] 2300292749_63109239
- [ ] 230029277_63109247
- [
] 2300294712_63109236
- [ ] 2300308032_63111581
- [ ] 2300323537_63114209
- [ ] 2300334609_63115535
- [ ] 2300346867_63118093
- [ ] 2300346867_63118093_NA12878
- [ ] 2300348940_63118099
- [ ] 2300359806_63119915
- [ ] 2300380476_63123963
- [ ] 2300382582_63123749
- [ ] 2300384269_63126867
- [ ] 2300407581_63130826
- [ ] 2300407626_63130842
- [ ] 2300409593_63130874
- [ ] 2300409612_63130980
- [ ] 2300417623_63131524
** TODO Variants manqués :missed:
SCHEDULED: <2023-10-21 Sat>
*** DONE 63012582: chr10:g.102230760 filtré par AD :63012582:
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
Il est en sortie d'haplotypecaller !
Attention à la position : POS=102230753 noté CG->C
GT:AD:DP:GQ:PL 0/1:26,8:34:99:146,0,671
Filtré par la condition AD <= 10 (porté par 8 reads seulement)
Non confirméen sanger, rendu vous
**** KILL image BAM cento
CLOSED: [2023-10-08 Sun 23:13]
**** DONE image BAM bisonex
CLOSED: [2023-10-08 Sun 23:23] SCHEDULED: <2023-10-08 Sun>
**** DONE Mail Paul
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
*** DONE 63060439: chr15:g.26869324 = Problème de profondeur DP=15 :63060439:
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
GABRA5
Rendu VOUS avec un variant patho MDB5 pour même patient (VOUS- même)
Non confirmé en Sanger
GT:AD:DP:GQ:PL 0/1:9,6:15:99:103,0,213
**** DONE image BAM bisonex
CLOSED: [2023-10-08 Sun 22:56]
**** DONE Mail Paul
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
** TODO Comparer variants cento à sortie bisonex :checkpipeline:
SCHEDULED: <2023-10-21 Sat>
*** TODO Un seul exécutable pour toutes les étapes
SCHEDULED: <2023-10-21 Sat>
Un utilitaire en ligne de commande qui appel les différentes étapes.
On utilise une structure unique pour toutes les étapes mais qui sera remplie au fur et à mesure. En stockant dans un csv à chaque étape
**** DONE parse variants
CLOSED: [2023-10-21 Sat 23:29] SCHEDULED: <2023-10-21 Sat>
**** DONE Ajouter négatifs dans la liste des variants
CLOSED: [2023-10-22 Sun 23:01] SCHEDULED: <2023-10-21 Sat>
**** DONE Mettre à jour liste des variants
CLOSED: [2023-10-22 Sun 23:01] SCHEDULED: <2023-10-21 Sat>
- [X] Régéner la liste des variants
- [ ] Retrouver les variants modifié à la main avec diff
On ne garde que les ajouts
#+begin_src sh
awk -F ',' '{print $1","$2":"$3$4$5}' extracted.csv | ^sort | save -f extracted_concat.csv
xsv select 1-2 ~/annex/data/centogene/variants/variant_genomic.csv | ^sort | save variant_genomic_corr.csv -f
diff extracted_concat.csv variant_genomic_corr.csv | grep '^>' | save -f update.diff
#+end_src
- [X] Ajouter négatifs
345 variants non trouvés avant modification
141 après modification
- [X] Ajouter différence
- [X] Corriger erreurs de parsing
**** KILL Lifter coordonées variants cento génomique en GRCh38
CLOSED: [2023-10-21 Sat 22:47]
**** DONE Un seul type de données
CLOSED: [2023-10-25 Wed 09:13] SCHEDULED: <2023-10-21 Sat>
**** KILL variant_recoder pour avoir les coordonnées VCF
CLOSED: [2023-10-25 Wed 09:13] SCHEDULED: <2023-10-21 Sat>
mobidetails n e trouve pas les ieux transcrits
**** DONE Annotation mobidetails (gene + données gonémique)
CLOSED: [2023-10-25 Wed 09:14]
**** DONE Envoyer liste à Paul
SCHEDULED: <2023-10-26 Thu>
**** TODO compare chaque variant avec la sortie du pipeline
SCHEDULED: <2023-10-21 Sat>
Données brutes
#+begin_src
ls ~/annex/data/bisonex/annotate/full/ | wc -l
261
#+end_src
Parmis les variant annotaté :
#+begin_src sh
cabal run -- checkpipeline search -i variant_annotated.csv -d ~/annex/data/bisonex/annotate/full/ | save out.txt -f
#+end_src
Positifs retrouvés (nombre de patient)
#+begin_src
❯ rg '\\? True' out.txt | rg '"6\d+' -o | sed 's/"//' | ^sort | ^uniq | wc -l
98
#+end_src
Positifs manqués
#+begin_src
❯ rg '\\? False' out.txt | rg '"6\d+' -o | sed 's/"//' | ^sort | ^uniq | wc -l
5
#+end_src
Et les négatifs ?
#+begin_src sh
open variant_extracted.csv | where transcript == negatif | get file | split column ' ' | get column1 | sort | uniq | save negatif.txt -f
ls ~/annex/data/bisonex/annotate/full/ | get name | path basename | split column '-' | get column2 | split column '_' | get column1 | sort | uniq | save -f raw.txt
comm -12 negatif.txt raw.txt | wc -l
136
#+end_src
- 98 positifs retrouvés
- 5 manqué
- 136 rendus négatifs
Total: 239
A faire : chercher le variant pour chaque run
**** TODO confirme ou non en Sanger
SCHEDULED: <2023-10-21 Sat>
* Résultats
** TODO Speed-up BWA-mem
SCHEDULED: <2023-10-29 Sun>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-10-29 Sun>
* Communication
** DONE Mail NGS-diag
CLOSED: [2023-10-06 Fri 08:04] SCHEDULED: <2023-10-06 Fri>
/Entered on/ [2023-10-04 Wed 19:33]
from summarising data in this way. "
**** DONE Mail alexis
CLOSED: [2023-08-20 Sun 13:45] SCHEDULED: <2023-08-20 Sun>
**** TODO Données simuscop 200x
SCHEDULED: <2023-11-04 Sat>
**** DONE En T2T avec liftover (filtre = spip) : ok mais lent et trop de variants :tests:
CLOSED: [2023-09-17 Sun 17:13] SCHEDULED: <2023-09-17 Sun>
1. Conversion en bed
#+begin_src sh :dir:~/code/sanger
open snvs-cento-sanger.csv | select chrom pos | insert pos2 {$in.pos } | to csv --separator="\t" | save snvs-cento-sanger.bed -f
#+end_src
2. Liftover avec UCSC (en ligne)
NB: vérifié sur le premier résultat en cherche le read contenant le variant (samtools view -r puis samtools view | grep en T2T) et avec l'aide d'IGV, on a un variant qui correspond en
chr1:10757746
3. En supposant que l'ordre des variants n'a pas changé, on ajoute simplement REF et ALT avec annotateLifted.jl
Annotation spip *très lente* : 1h13 !
Résultat:
2×3 DataFrame
Row │ variant meanQual depth
│ String Float64 Int64
─────┼──────────────────────────────────────
1 │ chr12:g.13594572 60.0 1
2 │ chr17:g.10204026 60.0 1
144 found over 146
filter depth : another 0 missed variants
filter poly : another 0 missed variants
filter vep : another 0 missed variants
Et on a trop de variants en sortie (7330 !)
**** DONE Mail Paul avec résultats filtre en T2T + nouveau schéma
CLOSED: [2023-09-17 Sun 23:15] SCHEDULED: <2023-09-17 Sun>
** TODO Medically relevant genes
SCHEDULED: <2023-11-02 Thu>
/Entered on/ [2023-10-18 Wed 22:37]
* Ré-interprétation :reanalysis:
** DONE Lancer tests sur données brutes [225/250] <(samples.csv)> <(runs.waiting)>
CLOSED: [2023-10-14 Sat 11:58] SCHEDULED: <2023-10-08 Sun>
- [X] 100222_63015289
- [X] 1600304839_63051311
- [X] 1900007827_62913191
- [X] 1900398899_62999500
- [X] 1900486799_62913197
- [X] 2100422923_62952677
- [X] 2100458888_62933047
- [X] 2100601558_62903840
- [X] 2100609288_62905768
- [X] 2100609501_62905776
- [X] 2100614493_62951074
- [X] 2100622566_62908067
- [X] 2100622601_62908060
- [X] 2100622705_62908063
- [X] 2100640027_62911936
- [X] 2100645285_62913212
- [X] 2100661411_62914081
- [X] 2100661462_62914086
- [X] 2100708257_62921596
- [X] 2100738732_62926501
- [X] 2100738850_62926509
- [X] 2100746751_62926505
- [X] 2100746797_62926506
- [X] 2100782349_62931722
- [X] 2100782416_62931561
- [X] 2100782559_62931718
- [X] 2100799204_62934768
- [X] 2200010202_62940284
- [X] 2200023600_62940631
- [X] 2200024348_62999591
- [X] 2200027505_62942457
- [X] 2200038776_62943412
- [X] 2200041919_62943405
- [X] 2200088014_62951326
- [X] 2200146652_62959388
- [X] 2200151850_62960953
- [X] 2200160014_62959475
- [X] 2200160070_62959478
- [X] 2200201368_62967471
- [X] 2200201400_62967470
- [X] 2200265558_62976332
- [X] 2200265605_62976401
- [X] 2200267046_62975192
- [X] 2200273878_62999530
- [X] 2200279708_62977002
- [X] 2200284408_62979102
- [X] 2200293987_62979116
- [X] 2200294359_62979118
- [X] 2200306299_62982217
- [X] 2200306539_62982193
- [X] 220030671_62982211
- [X] 2200307058_62982231
- [X] 2200307108_62982196
- [X] 2200307136_62982221
- [X] 2200307199_62982239
- [X] 2200307230_62982234
- [X] 2200307262_62982219
- [X] 2200307297_62982227
- [X] 2200324510_62985453
- [X] 2200324549_62985478
- [X] 2200324573_62985445
- [X] 2200324594_62985467
- [X] 2200324606_62985463
- [X] 2200324614_62985459
- [X] 2200338306_62985430
- [X] 2200343880_62989407
- [X] 2200343910_62989460
- [X] 2200343938_62989451
- [X] 2200343966_62989456
- [X] 2200343993_62989440
- [X] 2200344013_62989464
- [X] 2200349749_62989465
- [X] 2200363462_62988848
- [X] 2200377880_62991993
- [X] 2200378032_62991991
- [X] 2200383996_62993828
- [X] 2200384015_62993796
- [X] 2200384046_62993822
- [X] 2200384117_62993808
- [X] 2200384187_62993825
- [X] 2200384231_62992898
- [X] 2200385658_63060260
- [X] 2200394260_62994732
- [X] 2200395817_62994742
- [X] 2200396731_62994737
- [X] 2200424073_62999579
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- [X] 2200441970_63000868
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- [X] 2200775505_63060410
- [X] 2200850441_63019345
- [X] 220597589_63026879
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- [X] 2300103609_63076239
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- [X] 2300109602_63076765
- [X] 2300109665_63076770
- [X] 2300119721_63078732
- [X] 2300137773_63078133
- [X] 2300137834_63078123
- [X] 2300167821_63086183
- [X] 2300172698_63113453
- [X] 2300188216_63090609
- [X] 2300188281_63090632
- [ ] 2300188800_63090616
- [ ] 2300193193645_63090623
- [ ] 2300193668_63090611
- [ ] 2300195426_63090608
- [ ] 2300201017_63089636
- [ ] 2300227479_63098330
- [ ] 2300232688_63130821
- [ ] 2300292749_63109239
- [ ] 230029277_63109247
- [ ] 2300294712_63109236
- [ ] 2300308032_63111581
- [ ] 2300323537_63114209
- [ ] 2300334609_63115535
- [ ] 2300346867_63118093
- [ ] 2300346867_63118093_NA12878
- [ ] 2300348940_63118099
- [ ] 2300359806_63119915
- [ ] 2300380476_63123963
- [ ] 2300382582_63123749
- [ ] 2300384269_63126867
- [ ] 2300407581_63130826
- [ ] 2300407626_63130842
- [ ] 2300409593_63130874
- [ ] 2300409612_63130980
- [ ] 2300417623_63131524
** TODO Variants manqués :missed:
SCHEDULED: <2023-10-21 Sat>
*** DONE 63012582: chr10:g.102230760 filtré par AD :63012582:
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
Il est en sortie d'haplotypecaller !
Attention à la position : POS=102230753 noté CG->C
GT:AD:DP:GQ:PL 0/1:26,8:34:99:146,0,671
Filtré par la condition AD <= 10 (porté par 8 reads seulement)
Non confirméen sanger, rendu vous
**** KILL image BAM cento
CLOSED: [2023-10-08 Sun 23:13]
**** DONE image BAM bisonex
CLOSED: [2023-10-08 Sun 23:23] SCHEDULED: <2023-10-08 Sun>
**** DONE Mail Paul
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
*** DONE 63060439: chr15:g.26869324 = Problème de profondeur DP=15 :63060439:
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
GABRA5
Rendu VOUS avec un variant patho MDB5 pour même patient (VOUS- même)
Non confirmé en Sanger
GT:AD:DP:GQ:PL 0/1:9,6:15:99:103,0,213
**** DONE image BAM bisonex
CLOSED: [2023-10-08 Sun 22:56]
**** DONE Mail Paul
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
** TODO Comparer variants cento à sortie bisonex :checkpipeline:
SCHEDULED: <2023-10-21 Sat>
*** TODO Un seul exécutable pour toutes les étapes
SCHEDULED: <2023-10-21 Sat>
Un utilitaire en ligne de commande qui appel les différentes étapes.
On utilise une structure unique pour toutes les étapes mais qui sera remplie au fur et à mesure. En stockant dans un csv à chaque étape
**** DONE parse variants
CLOSED: [2023-10-21 Sat 23:29] SCHEDULED: <2023-10-21 Sat>
**** DONE Ajouter négatifs dans la liste des variants
CLOSED: [2023-10-22 Sun 23:01] SCHEDULED: <2023-10-21 Sat>
**** DONE Mettre à jour liste des variants
CLOSED: [2023-10-22 Sun 23:01] SCHEDULED: <2023-10-21 Sat>
- [X] Régéner la liste des variants
- [ ] Retrouver les variants modifié à la main avec diff
On ne garde que les ajouts
#+begin_src sh
awk -F ',' '{print $1","$2":"$3$4$5}' extracted.csv | ^sort | save -f extracted_concat.csv
xsv select 1-2 ~/annex/data/centogene/variants/variant_genomic.csv | ^sort | save variant_genomic_corr.csv -f
diff extracted_concat.csv variant_genomic_corr.csv | grep '^>' | save -f update.diff
#+end_src
- [X] Ajouter négatifs
345 variants non trouvés avant modification
141 après modification
- [X] Ajouter différence
- [X] Corriger erreurs de parsing
**** KILL Lifter coordonées variants cento génomique en GRCh38
CLOSED: [2023-10-21 Sat 22:47]
**** DONE Un seul type de données
CLOSED: [2023-10-25 Wed 09:13] SCHEDULED: <2023-10-21 Sat>
**** KILL variant_recoder pour avoir les coordonnées VCF
CLOSED: [2023-10-25 Wed 09:13] SCHEDULED: <2023-10-21 Sat>
mobidetails n e trouve pas les ieux transcrits
**** DONE Annotation mobidetails (gene + données gonémique)
CLOSED: [2023-10-25 Wed 09:14]
**** DONE Envoyer liste à Paul
SCHEDULED: <2023-10-26 Thu>
**** TODO compare chaque variant avec la sortie du pipeline
SCHEDULED: <2023-10-21 Sat>
Avec la fonction "test" dans Search.hs
1126 extracted
654 annotated
253 raw data
102 raw and annotated
236 raw and extracted
17 raw NOT extracted
890 extract WITHOUT raw
#+begin_src sh
❯ open diff.txt | from csv | get id | into string | each {|e| "~/annex/data/centogene/reports/" ++ $e ++ "*.pdf"} | each {|e| firefox $e }
#+end_src
Les 17 manquants sont
- 62913191 : CNV
- 62959388 : MT-ATP6
- 62999572 : MT-ATP6
- 62999627 : CNV
- 62999630 : CNV
- 63004218: CNV
- 63006466 : CNV
- 63009152 : manqué à extraire
- 63015289: CNV
- 63024910 : MT-ATP6
- 63040251 : CNV
- 63043050 : CNV
- 63118093 : NA12878
- NA12878 x4
A faire : chercher le variant pour chaque run
**** TODO confirme ou non en Sanger
SCHEDULED: <2023-10-21 Sat>
* Résultats
** TODO Speed-up BWA-mem
SCHEDULED: <2023-11-04 Sat>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-11-04 Sat>
* Communication
** DONE Mail NGS-diag
CLOSED: [2023-10-06 Fri 08:04] SCHEDULED: <2023-10-06 Fri>
/Entered on/ [2023-10-04 Wed 19:33]