B:BD[
2.24725] → [
2.24725:28443]
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
**** TODO [#A] Tout insérer dans NA12878 avec XAMscissors (XAMScissors à jour)
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>
***** TODO Vérifier après filter vep: 26 perdus
SCHEDULED: <2023-08-20 Sun>
Row │ variant meanQual depth
│ String Float64 Int64
─────┼───────────────────────────────────────
1 │ chr1:g.183222115C>T 60.0 124
2 │ chr1:g.39388062C>T 60.0 136
3 │ chr2:g.240719197G>C 60.0 98
4 │ chr3:g.41227353G>C 60.0 93
5 │ chr4:g.15536991T>G 59.6584 161
6 │ chr5:g.14474096G>A 60.0 96
7 │ chr8:g.43122149C>T 60.0 134
8 │ chr9:g.128603589A>C 60.0 104
9 │ chr9:g.137452819G>C 60.0 156
10 │ chr10:g.129957338T>C 60.0 67
11 │ chr10:g.247389T>G 60.0 79
12 │ chr11:g.61313668G>A 60.0 69
13 │ chr12:g.45850467C>T 60.0 90
14 │ chr14:g.58458545G>A 60.0 51
15 │ chr14:g.64216315C>G 60.0 167
16 │ chr15:g.60514655G>A 60.0 113
17 │ chr15:g.66703292C>T 60.0 95
18 │ chr17:g.61966475G>T 60.0 67
19 │ chr17:g.7852503T>C 60.0 96
20 │ chr19:g.13230158G>A 60.0 135
21 │ chr19:g.38523211C>G 60.0 180
22 │ chr19:g.4110557G>C 60.0 219
23 │ chr20:g.62334188G>A 60.0 94
24 │ chrX:g.24737739G>T 60.0 76
25 │ chrX:g.47575255G>A 60.0 145
26 │ chrX:g.53409112G>A 60.0 186
**** TODO Données simuscop 200x
SCHEDULED: <2023-08-22 Tue>
* Résultats
** TODO Speed-up BWA-mem
SCHEDULED: <2023-08-26 Sat>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-08-26 Sat>
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: <2023-08-22 Tue>
* Résultats
** TODO Speed-up BWA-mem
SCHEDULED: <2023-08-26 Sat>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-08-26 Sat>