3×3 DataFrame
| variant | meanQual | depth |
|---------------------+----------+-------|
| chr12:g.13720138C>T | 60.0 | 1 |
| chr17:g.10296150T>A | 60.0 | 3 |
| chr21:g.43426167C>T | 0.0 | 88 |
Pas assez de read (1,2) et problème d'alignement (3)
***** KILL Résultat après filtre depth : +10 variants perduis
CLOSED: [2023-08-19 Sat 20:04] SCHEDULED: <2023-08-18 Fri>
filter depth : another 10 missed variants
10×3 DataFrame
| variant | meanQual | depth |
|---------------------+----------+-------|
| chr3:g.71112628C>T | 60.0 | 62 |
| chr12:g.40367710A>G | 58.0435 | 46 |
| chr14:g.58458545G>A | 60.0 | 9 |
| chr15:g.66703292C>T | 60.0 | 33 |
| chr16:g.30965737C>A | 60.0 | 18 |
| chr17:g.61968202A>C | 60.0 | 46 |
| chrX:g.124056226T>G | 60.0 | 40 |
| chrX:g.24737739G>T | 60.0 | 16 |
| chrX:g.40591349C>T | 60.0 | 37 |
| chrX:g.53193275G>A | 60.0 | 32 |
| | | |
S'ils sont hétérozygotes, 0.5*depth est effectivement < 30 (notre filtre...)
****** KILL Problème d'inserstion des reads: on en perd de nombreux ! -> regénérer données
CLOSED: [2023-08-19 Sat 20:04] SCHEDULED: <2023-08-18 Fri>
Ex: chrX:g.124056226T>G : on passe de 65 reads à 1
***** DONE Résultat après filtre common variant: +0 ok
CLOSED: [2023-08-17 Thu 19:32]
***** KILL Résultat après filtre VEP : +23 perdus ??
CLOSED: [2023-08-19 Sat 20:04] SCHEDULED: <2023-08-18 Fri>
filter vep : another 23 missed variants
23×3 DataFrame
Row │ variant meanQual depth
│ String Float64 Int64
─────┼───────────────────────────────────────
1 │ chr1:g.183222115C>T 60.0 168
2 │ chr1:g.39388062C>T 60.0 285
3 │ chr2:g.240719197G>C 60.0 77
4 │ chr3:g.41227353G>C 60.0 105
5 │ chr4:g.15536991T>G 60.0 41
6 │ chr5:g.14474096G>A 60.0 191
7 │ chr8:g.43122149C>T 60.0 237
8 │ chr9:g.128603589A>C 60.0 304
9 │ chr9:g.137452819G>C 60.0 107
10 │ chr10:g.129957338T>C 60.0 116
11 │ chr10:g.247389T>G 60.0 56
12 │ chr11:g.61313668G>A 60.0 83
13 │ chr12:g.45850467C>T 60.0 291
14 │ chr14:g.64216315C>G 60.0 263
15 │ chr15:g.60514655G>A 60.0 259
16 │ chr17:g.61966475G>T 60.0 144
17 │ chr17:g.7852503T>C 60.0 190
18 │ chr19:g.13230158G>A 60.0 172
19 │ chr19:g.38523211C>G 60.0 93
20 │ chr19:g.4110557G>C 59.9929 425
21 │ chr20:g.62334188G>A 60.0 62
22 │ chrX:g.47575255G>A 60.0 244
23 │ chrX:g.53409112G>A 60.0 136
**** DONE [#A] Tout insérer dans NA12878 avec XAMscissors (XAMScissors à jour)
CLOSED: [2023-08-20 Sun 13:45] SCHEDULED: <2023-08-19 Sat>
***** DONE Insertion
CLOSED: [2023-08-20 Sun 09:15]
***** DONE Vérifier après haplotypecaller: 3 variants manquant mais ok
CLOSED: [2023-08-20 Sun 09:18] SCHEDULED: <2023-08-20 Sun>
3×3 DataFrame
Row │ variant meanQual depth
│ String Float64 Int64
─────┼──────────────────────────────────────
1 │ chr12:g.13720138C>T 60.0 1
2 │ chr17:g.10296150T>A 60.0 1
3 │ chr21:g.43426167C>T 0.0 59
Manque de profondeur sur 2 et mauvaise qualité sur 3
***** DONE Vérifier après filterdepth: 0 perdus en plus
CLOSED: [2023-08-20 Sun 09:18] SCHEDULED: <2023-08-20 Sun>
***** DONE Vérifier après filterpolymorphis : 0 perdus en plus
CLOSED: [2023-08-20 Sun 09:18] SCHEDULED: <2023-08-20 Sun>
***** DONE Vérifier après filter vep: 2 perdus en plus
CLOSED: [2023-08-20 Sun 12:37] SCHEDULED: <2023-08-20 Sun>
2×3 DataFrame
Row │ variant meanQual depth
│ String Float64 Int64
─────┼─────────────────────────────────────
1 │ chr17:g.7852503T>C 60.0 96
2 │ chrX:g.47575255G>A 60.0 145
***** DONE 1ere correction spip: meilleur nombre de variants en sortie mais manque toujours ces 2
CLOSED: [2023-08-20 Sun 11:38]
***** DONE --pick : résout le problème
CLOSED: [2023-08-20 Sun 12:37]
chrX:g.47575255G>A est rendu downstream_gene_variant avec l'option --pick
Or il n'est pas en5' dans les transcrits refseq...
https://genome-euro.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chrX%3A47575242%2D47575268&hgsid=301211823_xpelPqPJije7wSIhg070JeGH5ZwV
https://mobidetails.iurc.montp.inserm.fr/MD/api/variant/238296/browser/
Idem pour l'autre
chr17:g.7852503T>C
https://mobidetails.iurc.montp.inserm.fr/MD/api/variant/182993/browser/
Note:
VEP chooses one block of annotation per variant, using an ordered set of criteria. This order may be customised using --pick_order.
MANE Select transcript status
MANE Plus Clinical transcript status
canonical status of transcript
APPRIS isoform annotation
transcript support level
biotype of transcript ("protein_coding" preferred)
CCDS status of transcript
consequence rank according to this table
translated, transcript or feature length (longer preferred)
"Wherever possible we would discourage you 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: <2023-10-18 Wed>
**** 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>
* 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
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- [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>
* Résultats
** TODO Speed-up BWA-mem
SCHEDULED: <2023-10-15 Sun>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-10-15 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]