apraga/org - Change QGZPAO3X5YZ7HFTQUJULRFCKRZXFOMJ23W3DNLMZZH4IVHUN7CSAC

Bisonex update

Created by Alexis Praga on September 29, 2023

QGZPAO3X5YZ7HFTQUJULRFCKRZXFOMJ23W3DNLMZZH4IVHUN7CSAC

Dependencies

In channels

main

Change contents

Replacement in projects.org at line 34 [5.123895]
∅:D[3.42] → [4.42:59]
B:BD[4.42] → [4.42:59]
```
**** TODO Projet
```
[3.42]
[3.43]
```
**** TODO Projet "~/documents/interchu-grenoble-projet.tex"
```

Replacement in projects/bisonex.org at line 28 [6.35]

B:BD[2.40959] → [2.40959:43287]

∅:D[2.43287] → [7.18528:24392]

B:BD[7.18528] → [7.18528:24392]

: <2023-08-30 Wed>
**** DONE Corriger spliceAI
CLOSED: [2023-08-31 Thu 13:51] SCHEDULED: <2023-08-31 Thu>
Pas d'annotation
- chromosome ? essai 1 au lieu de chr1 : idem. Et fonctionne pour CADD
- index ?
  - retélécharger
  - indexer nous-meme
**** DONE Supprimer score spip en double
CLOSED: [2023-08-31 Thu 14:17] SCHEDULED: <2023-08-31 Thu>
**** DONE Vérifier variant 63126867
CLOSED: [2023-08-31 Thu 10:52] SCHEDULED: <2023-08-31 Thu>
**** DONE Ajouter tronquant ou non
CLOSED: [2023-08-31 Thu 22:08] SCHEDULED: <2023-08-31 Thu>
**** DONE Ajouter récessif
CLOSED: [2023-08-31 Thu 22:08] SCHEDULED: <2023-08-31 Thu>
**** KILL Corriger allelic depth
CLOSED: [2023-08-31 Thu 11:18] SCHEDULED: <2023-08-31 Thu>
Problème lié à libre office
**** DONE Regénérer annotation pour na12878, inserted et patient PEX1
CLOSED: [2023-08-31 Thu 22:08] SCHEDULED: <2023-08-31 Thu>
**** TODO ACMG incidental
**** DONE Sortie VCF (pour avoir la fraction allélique AF)
CLOSED: [2023-08-28 Mon 17:22]
**** DONE VCF -> tsv avec bcftools
CLOSED: [2023-08-29 Tue 11:03] SCHEDULED: <2023-08-28 Mon>
**** DONE Un seul transcrit après VEP avec filter_vep :filter:
CLOSED: [2023-08-29 Tue 11:03] SCHEDULED: <2023-08-28 Mon>
Avec mise à jour VEP 110, pick_flag semble fonctionner.
***** DONE Test chr20: Pas de variant "perdus"
CLOSED: [2023-08-28 Mon 17:31] SCHEDULED: <2023-08-28 Mon>
contrairement au résultat communiqué à alexis par mail
#+begin_src sh :dir out/annotate
bcftools +counts vep/NA12878-sanger-chr20-GRCh38/NA12878-sanger-chr20-GRCh38.vep.vcf.gz
#+end_src
Number of samples: 1
Number of SNPs:    123
Number of INDELs:  32
Number of MNPs:    53
Number of others:  0
Number of sites:   208
#+begin_src  sh
filter_vep -i vep/NA12878-sanger-chr20-GRCh38/NA12878-sanger-chr20-GRCh38.vep.vcf.gz  --filter 'PICK' | bcftools +counts
#+end_src
Number of samples: 1
Number of SNPs:    123
Number of INDELs:  32
Number of MNPs:    53
Number of others:  0
Number of sites:   208
2nd vérification
#+begin_src sh :dir out/annotate
 filter_vep -i vep/NA12878-sanger-chr20-GRCh38/NA12878-sanger-chr20-GRCh38.vep.vcf.gz  --filter 'PICK' --soft_filter | grep fail
#+end_src
***** DONE Test NA12878 + variants sanger : variants perdus avec --pick ?
CLOSED: [2023-08-29 Tue 1
0:36] SCHEDULED: <2023-08-28 Mon>
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/out/annotate
~/.nix-profile/bin/bcftools +counts vep/NA12878-sanger-all-GRCh38/NA12878-sanger-all-GRCh38.vep.vcf.gz
#+end_src
#+RESULTS:
| Number | of | samples: |    1 |
| Number | of | SNPs:    | 6293 |
| Number | of | INDELs:  | 1515 |
| Number | of | MNPs:    | 1588 |
| Number | of | others:  |    0 |
| Number | of | sites:   | 9322 |
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/out/annotate
~/.nix-profile/bin/filter_vep -i vep/NA12878-sanger-all-GRCh38/NA12878-sanger-all-GRCh38.vep.vcf.gz  --filter 'PICK' | bcftools +counts
#+end_src
| Number | of | samples: |    1 |
| Number | of | SNPs:    | 6293 |
| Number | of | INDELs:  | 1515 |
| Number | of | MNPs:    | 1588 |
| Number | of | others:  |    0 |
| Number | of | sites:   | 9322 |
***** DONE Test NA12878 + variants sanger: vérifier sortie avec julia : ok
CLOSED: [2023-08-29 Tue 10:21] SCHEDULED: <2023-08-28 Mon>
143 variants/146 comme avant
***** DONE Relancer en T2T pour vérifier compatibilité :T2T:
CLOSED: [2023-08-29 Tue 11:03] SCHEDULED: <2023-08-29 Tue>
**** DONE Repasser les tests sanger sur NA12878
CLOSED: [2023-09-01 Fri 10:32] SCHEDULED: <2023-08-31 Thu>
2 variants manquants après filter vep
**** DONE Choisir le meilleur transcript nous-meme
CLOSED: [2023-09-01 Fri 10:32] SCHEDULED: <2023-09-01 Fri>
**** DONE Vérifier T2T passe
CLOSED: [2023-08-31 Thu 22:10] SCHEDULED: <2023-08-31 Thu>
**** DONE Revoir choix du transcrit + filtre  avec paul
CLOSED: [2023-09-08 Fri 22:46] SCHEDULED: <2023-09-06 Wed>
**** DONE Filtrer les variants selon les filtres d'Alexis et garder tous les résultat
CLOSED: [2023-09-10 Sun 15:39] SCHEDULED: <2023-09-09 Sat>
**** DONE Ajout colonne MANE SELECT et garder les autres
CLOSED: [2023-09-10 Sun 15:39] SCHEDULED: <2023-09-09 Sat>
**** DONE v1.0
CLOSED: [2023-09-11 Mon 19:11] SCHEDULED: <2023-09-09 Sat>
***** DONE Branche prod
CLOSED: [2023-09-10 Sun 15:44] SCHEDULED: <2023-09-09 Sat>
Merge depuis debug
***** DONE Mail alexis
CLOSED: [2023-09-01 Fri 10:32] SCHEDULED: <2023-08-31 Thu>
***** DONE Relancer test sanger
CLOSED: [2023-09-11 Mon 19:11] SCHEDULED: <2023-09-10 Sun>
***** DONE Mail Paul pour validation
CLOSED: [2023-09-11 Mon 19:11] SCHEDULED: <2023-09-10 Sun>
**** DONE Utiliser spliceAI >= 0.2 pour filtre au lieu de spip
CLOSED: [2023-09-11 Mon 21:48] SCHEDULED: <2023-09-11 Mon>
**** DONE Repasser tests sanger avec spliceAI
CLOSED: [2023-09-14 Thu 22:45] SCHEDULED: <2023-09-11 Mon>
**** DONE Corriger colonne récessive
CLOSED: [2023-09-14 Thu 22:57] SCHEDULED: <2023-09-14 Thu>
soit 1/1, soit 1/2
soit 0/1 avec 2 variants par gene
*** KILL Comparer les annotations sur 63003856
CLOSED: [2023-08-28 Mon 17:28]
**** Relancer le nouveau pipeline
*** KILL Ancienne version
CLOSED: [2023-08-28 Mon 17:24]
**** KILL HGVS
CLOSED: [2023-08-28 Mon 17:24]
**** KILL Filtrer après VEP
CLOSED: [2023-08-28 Mon 17:24]
**** KILL OMIM
CLOSED: [2023-08-28 Mon 17:24]
**** KILL clinvar
CLOSED: [2023-08-28 Mon 17:24]
**** KILL ACMG incidental
CLOSED: [2023-08-28 Mon 17:24]
**** KILL Grantham
CLOSED: [2023-08-28 Mon 17:24]
**** KILL LRG
CLOSED: [2023-04-18 mar. 17:22] SCHEDULED: <2023-04-18 Tue>
Vu avec alexis, n’est plus à jour
**** KILL Gnomad
CLOSED: [2023-08-28 Mon 17:24]
*** DONE Réordonner les colonnes :annotation:
CLOSED: [2023-08-31 Thu 10:38] SCHEDULED: <2023-08-28 Mon>
Pas d'OMIM, pas de CADD, pas de spliceAI
** DONE Porter exactement la version d'Alexis sur Helios
CLOSED: [2023-01-14 Sat 17:56]
Branche "prod"
** KILL Tester version d'alexis avec Nix
CLOSED: [2023-06-14 Wed 22:37]
*** DONE Ajouter clinvar
CLOSED: [2022-11-13 Sun 19:37]
*** DONE Alignement
CLOSED: [2022-11-13 Sun 12:52]
*** DONE Haplotype caller
CLOSED: [2022-11-13 Sun 13:00]
*** KILL Filter
CLOSED: [2023-06-14 Wed 22:37]
- [X] depth
- [ ] comon snp not path
Problème avec liste des ID
**** KILL variant annotation
CLOSED: [2023-06-14 Wed 22:37]
Besoin de vep
*** KILL Variant calling
CLOSED: [2023-06-14 Wed 22:37]
** KILL Tester sarek
CLOSED: [2023-08-12 Sat 15:53]
#+begin_src sh
 module load apptainer/1.1.8
 nextflow run nf-core/sarek -profile test,singularity --outdir test-sarek
#+end_src
Les dépendences ne se téléchargent pas correctement, on les extrait à la main
#+begin_src sh
 rg -IN galaxyproject modules  | sed 's/ //g;s/:$//' | sort | uniq > deps.txt
#+end_src
 Nettoyage à la main
 Puis
 #+begin_src sh
 cat deps.txt | xargs -L1 singularity pull
 #+end_src
** DONE Support pour samplesheet
CLOSED: [2023-08-03 Thu 14:24] SCHEDULED: <2023-08-03 Thu 13:00>
/Entered on/ [2023-08-03 Thu 13:12]
** DONE Petit jeu de données : chr22 sur HG001
CLOSED: [2023-08-05 Sat 14:21] SCHEDULED: <2023-08-05 Sat>
** DONE Corriger OMIM annotation: manquant pour NMNAT1
CLOSED: [2023-09-16 Sat 22:47] SCHEDULED: <2023-09-16 Sat>
/Entered on/ [2023-09-16 Sat 19:32]
* Documentation
:PROPERTIES:
:CATEGORY: doc
:END:
** DONE Procédure d'installation nix + dependences pour VM CHU
CLOSED: [2023-04-22 Sat 15:27] SCHEDULED: <2023-04-13 Thu>
* Bibliographie
** DONE Finir[cite:@alser2021]
CLOSED: [2023-09-26 Tue 11:26] SCHEDULED: <2023-09-22 Fri>
* Manuscript
:PROPERTIES:
:CATEGORY: manuscript
:END:
** DONE Flowchart pipeline (avec T2T)
CLOSED: [2023-09-17 Sun 23:15] SCHEDULED: <2023-09-17 Sun>
** DONE Figure: nombre de publication par aligneur
CLOSED: [2023-09-19 Tue 16:54] SCHEDULED: <2023-09-19 Tue>
/Entered on/ [2023-09-19 Tue 08:43]
** TODO Figure: nombre de publication par appel de variant
SCHEDULED: <2023-09-19 Tue>
/Entered on/ [2023-09-19 Tue 08:43]
** TODO Figure: nombre d'exomes par années
SCHEDULED: <2023-09-30 Sat>
/Entered on/ [20

[2.40959]

[7.24392]

: <2023-08-30 Wed>
**** DONE Corriger spliceAI
CLOSED: [2023-08-31 Thu 13:51] SCHEDULED: <2023-08-31 Thu>
Pas d'annotation
- chromosome ? essai 1 au lieu de chr1 : idem. Et fonctionne pour CADD
- index ?
  - retélécharger
  - indexer nous-meme
**** DONE Supprimer score spip en double
CLOSED: [2023-08-31 Thu 14:17] SCHEDULED: <2023-08-31 Thu>
**** DONE Vérifier variant 63126867
CLOSED: [2023-08-31 Thu 10:52] SCHEDULED: <2023-08-31 Thu>
**** DONE Ajouter tronquant ou non
CLOSED: [2023-08-31 Thu 22:08] SCHEDULED: <2023-08-31 Thu>
**** DONE Ajouter récessif
CLOSED: [2023-08-31 Thu 22:08] SCHEDULED: <2023-08-31 Thu>
**** KILL Corriger allelic depth
CLOSED: [2023-08-31 Thu 11:18] SCHEDULED: <2023-08-31 Thu>
Problème lié à libre office
**** DONE Regénérer annotation pour na12878, inserted et patient PEX1
CLOSED: [2023-08-31 Thu 22:08] SCHEDULED: <2023-08-31 Thu>
**** TODO ACMG incidental
**** DONE Sortie VCF (pour avoir la fraction allélique AF)
CLOSED: [2023-08-28 Mon 17:22]
**** DONE VCF -> tsv avec bcftools
CLOSED: [2023-08-29 Tue 11:03] SCHEDULED: <2023-08-28 Mon>
**** DONE Un seul transcrit après VEP avec filter_vep :filter:
CLOSED: [2023-08-29 Tue 11:03] SCHEDULED: <2023-08-28 Mon>
Avec mise à jour VEP 110, pick_flag semble fonctionner.
***** DONE Test chr20: Pas de variant "perdus"
CLOSED: [2023-08-28 Mon 17:31] SCHEDULED: <2023-08-28 Mon>
contrairement au résultat communiqué à alexis par mail
#+begin_src sh :dir out/annotate
bcftools +counts vep/NA12878-sanger-chr20-GRCh38/NA12878-sanger-chr20-GRCh38.vep.vcf.gz
#+end_src
Number of samples: 1
Number of SNPs:    123
Number of INDELs:  32
Number of MNPs:    53
Number of others:  0
Number of sites:   208
#+begin_src  sh
filter_vep -i vep/NA12878-sanger-chr20-GRCh38/NA12878-sanger-chr20-GRCh38.vep.vcf.gz  --filter 'PICK' | bcftools +counts
#+end_src
Number of samples: 1
Number of SNPs:    123
Number of INDELs:  32
Number of MNPs:    53
Number of others:  0
Number of sites:   208
2nd vérification
#+begin_src sh :dir out/annotate
 filter_vep -i vep/NA12878-sanger-chr20-GRCh38/NA12878-sanger-chr20-GRCh38.vep.vcf.gz  --filter 'PICK' --soft_filter | grep fail
#+end_src
***** DONE Test NA12878 + variants sanger : variants perdus avec --pick ?
CLOSED: [2023-08-29 Tue 10:36] SCHEDULED: <2023-08-28 Mon>
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/out/annotate
~/.nix-profile/bin/bcftools +counts vep/NA12878-sanger-all-GRCh38/NA12878-sanger-all-GRCh38.vep.vcf.gz
#+end_src
#+RESULTS:
| Number | of | samples: |    1 |
| Number | of | SNPs:    | 6293 |
| Number | of | INDELs:  | 1515 |
| Number | of | MNPs:    | 1588 |
| Number | of | others:  |    0 |
| Number | of | sites:   | 9322 |
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/out/annotate
~/.nix-profile/bin/filter_vep -i vep/NA12878-sanger-all-GRCh38/NA12878-sanger-all-GRCh38.vep.vcf.gz  --filter 'PICK' | bcftools +counts
#+end_src
| Number | of | samples: |    1 |
| Number | of | SNPs:    | 6293 |
| Number | of | INDELs:  | 1515 |
| Number | of | MNPs:    | 1588 |
| Number | of | others:  |    0 |
| Number | of | sites:   | 9322 |
***** DONE Test NA12878 + variants sanger: vérifier sortie avec julia : ok
CLOSED: [2023-08-29 Tue 10:21] SCHEDULED: <2023-08-28 Mon>
143 variants/146 comme avant
***** DONE Relancer en T2T pour vérifier compatibilité :T2T:
CLOSED: [2023-08-29 Tue 11:03] SCHEDULED: <2023-08-29 Tue>
**** DONE Repasser les tests sanger sur NA12878
CLOSED: [2023-09-01 Fri 10:32] SCHEDULED: <2023-08-31 Thu>
2 variants manquants après filter vep
**** DONE Choisir le meilleur transcript nous-meme
CLOSED: [2023-09-01 Fri 10:32] SCHEDULED: <2023-09-01 Fri>
**** DONE Vérifier T2T passe
CLOSED: [2023-08-31 Thu 22:10] SCHEDULED: <2023-08-31 Thu>
**** DONE Revoir choix du transcrit + filtre  avec paul
CLOSED: [2023-09-08 Fri 22:46] SCHEDULED: <2023-09-06 Wed>
**** DONE Filtrer les variants selon les filtres d'Alexis et garder tous les résultat
CLOSED: [2023-09-10 Sun 15:39] SCHEDULED: <2023-09-09 Sat>
**** DONE Ajout colonne MANE SELECT et garder les autres
CLOSED: [2023-09-10 Sun 15:39] SCHEDULED: <2023-09-09 Sat>
**** DONE v1.0
CLOSED: [2023-09-11 Mon 19:11] SCHEDULED: <2023-09-09 Sat>
***** DONE Branche prod
CLOSED: [2023-09-10 Sun 15:44] SCHEDULED: <2023-09-09 Sat>
Merge depuis debug
***** DONE Mail alexis
CLOSED: [2023-09-01 Fri 10:32] SCHEDULED: <2023-08-31 Thu>
***** DONE Relancer test sanger
CLOSED: [2023-09-11 Mon 19:11] SCHEDULED: <2023-09-10 Sun>
***** DONE Mail Paul pour validation
CLOSED: [2023-09-11 Mon 19:11] SCHEDULED: <2023-09-10 Sun>
**** DONE Utiliser spliceAI >= 0.2 pour filtre au lieu de spip
CLOSED: [2023-09-11 Mon 21:48] SCHEDULED: <2023-09-11 Mon>
**** DONE Repasser tests sanger avec spliceAI
CLOSED: [2023-09-14 Thu 22:45] SCHEDULED: <2023-09-11 Mon>
**** DONE Corriger colonne récessive
CLOSED: [2023-09-14 Thu 22:57] SCHEDULED: <2023-09-14 Thu>
soit 1/1, soit 1/2
soit 0/1 avec 2 variants par gene
*** KILL Comparer les annotations sur 63003856
CLOSED: [2023-08-28 Mon 17:28]
**** Relancer le nouveau pipeline
*** KILL Ancienne version
CLOSED: [2023-08-28 Mon 17:24]
**** KILL HGVS
CLOSED: [2023-08-28 Mon 17:24]
**** KILL Filtrer après VEP
CLOSED: [2023-08-28 Mon 17:24]
**** KILL OMIM
CLOSED: [2023-08-28 Mon 17:24]
**** KILL clinvar
CLOSED: [2023-08-28 Mon 17:24]
**** KILL ACMG incidental
CLOSED: [2023-08-28 Mon 17:24]
**** KILL Grantham
CLOSED: [2023-08-28 Mon 17:24]
**** KILL LRG
CLOSED: [2023-04-18 mar. 17:22] SCHEDULED: <2023-04-18 Tue>
Vu avec alexis, n’est plus à jour
**** KILL Gnomad
CLOSED: [2023-08-28 Mon 17:24]
*** DONE Réordonner les colonnes :annotation:
CLOSED: [2023-08-31 Thu 10:38] SCHEDULED: <2023-08-28 Mon>
Pas d'OMIM, pas de CADD, pas de spliceAI
*** TODO Ajouter gnomAD v3 :gnomadv3:
SCHEDULED: <2023-09-29 Fri>
/Entered on/ [2023-09-29 Fri 22:38]
Après discussion avec Mathieu sur le problème de certaines régions corrigées dans la v3 !
VEP utilise la v2 pour les exomes et v3 pour génomes
Il manquera pour les patients 1-107
On ne l'a pas dans la sortie de VEP jusque là
**** TODO Test sur 1 patient
SCHEDULED: <2023-09-29 Fri>
**** TODO Reprendre run batc
** DONE Porter exactement la version d'Alexis sur Helios
CLOSED: [2023-01-14 Sat 17:56]
Branche "prod"
** KILL Tester version d'alexis avec Nix
CLOSED: [2023-06-14 Wed 22:37]
*** DONE Ajouter clinvar
CLOSED: [2022-11-13 Sun 19:37]
*** DONE Alignement
CLOSED: [2022-11-13 Sun 12:52]
*** DONE Haplotype caller
CLOSED: [2022-11-13 Sun 13:00]
*** KILL Filter
CLOSED: [2023-06-14 Wed 22:37]
- [X] depth
- [ ] comon snp not path
Problème avec liste des ID
**** KILL variant annotation
CLOSED: [2023-06-14 Wed 22:37]
Besoin de vep
*** KILL Variant calling
CLOSED: [2023-06-14 Wed 22:37]
** KILL Tester sarek
CLOSED: [2023-08-12 Sat 15:53]
#+begin_src sh
 module load apptainer/1.1.8
 nextflow run nf-core/sarek -profile test,singularity --outdir test-sarek
#+end_src
Les dépendences ne se téléchargent pas correctement, on les extrait à la main
#+begin_src sh
 rg -IN galaxyproject modules  | sed 's/ //g;s/:$//' | sort | uniq > deps.txt
#+end_src
 Nettoyage à la main
 Puis
 #+begin_src sh
 cat deps.txt | xargs -L1 singularity pull
 #+end_src
** DONE Support pour samplesheet
CLOSED: [2023-08-03 Thu 14:24] SCHEDULED: <2023-08-03 Thu 13:00>
/Entered on/ [2023-08-03 Thu 13:12]
** DONE Petit jeu de données : chr22 sur HG001
CLOSED: [2023-08-05 Sat 14:21] SCHEDULED: <2023-08-05 Sat>
** DONE Corriger OMIM annotation: manquant pour NMNAT1
CLOSED: [2023-09-16 Sat 22:47] SCHEDULED: <2023-09-16 Sat>
/Entered on/ [2023-09-16 Sat 19:32]
* Documentation
:PROPERTIES:
:CATEGORY: doc
:END:
** DONE Procédure d'installation nix + dependences pour VM CHU
CLOSED: [2023-04-22 Sat 15:27] SCHEDULED: <2023-04-13 Thu>
* Bibliographie
** DONE Finir[cite:@alser2021]
CLOSED: [2023-09-26 Tue 11:26] SCHEDULED: <2023-09-22 Fri>
* Manuscript
:PROPERTIES:
:CATEGORY: manuscript
:END:
** DONE Flowchart pipeline (avec T2T)
CLOSED: [2023-09-17 Sun 23:15] SCHEDULED: <2023-09-17 Sun>
** DONE Figure: nombre de publication par aligneur
CLOSED: [2023-09-19 Tue 16:54] SCHEDULED: <2023-09-19 Tue>
/Entered on/ [2023-09-19 Tue 08:43]
** TODO Figure: nombre de publication par appel de variant
SCHEDULED: <2023-09-19 Tue>
/Entered on/ [2023-09-19 Tue 08:43]
** TODO Figure: nombre d'exomes par années
SCHEDULED: <2023-09-30 Sat>
/Entered on/ [20

Replacement in projects/bisonex.org at line 78 [6.35]

B:BD[7.40778] → [7.40778:48034]

 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
** TODO Lancer tests sur données brutes [87/250]
- [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
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- [ ] 2200699290_63043047
- [ ] 2200699345_63040238
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- [ ] 2200699412_63040731
- [ ] 220071551_63048935
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- [ ] 2200748145_63051198
- [ ] 2200748171_63051213
- [ ] 2200751046_63051249
- [ ] 2200751101_63051234
- [ ] 2200766471_63054590
- [ ] 2200767731_63054595
- [ ] 2200767822_63054464
- [ ] 2200775505_63060410
- [ ] 2200850441_63019345
- [ ] 220597589_63026879
- [ ] 2300003253_63060430
- [ ] 2300005679_63060370
- [ ] 2300009914_63060390
- [ ] 2300028784_63060001
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- [ ] 2300055382_63061874
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- [ ] 230006894_63064950
- [ ] 2300071111_63070356
- [ ] 2300083434_63071675
- [ ] 2300103609_63076239
- [ ] 2300104572_63076232
- [ ] 2300109602_63076765
- [ ] 2300109665_63076770
- [ ] 2300119721_63078732
- [ ] 2300137773_63078133
- [ ] 2300137834_63078123
- [ ] 2300167821_63086183
- [ ] 2300172698_63113453
- [ ] 2300188216_63090609
- [ ] 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
* Résultats
** TODO Speed-up BWA-mem
SCHEDULED: <2023-09-30 Sat>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-09-30 Sat>

[7.40778]

 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
** PROJ Lancer tests sur données brutes [107/250]
- [X] 100222_63015289
- [X] 1600304839_63051311
- [X] 1900007827_62913191
- [X] 1900398899_62999500
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- [ ] 2200533429_63060425
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- [ ] 2200614198_63113928
- [ ] 2200620372_63030821
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- [ ] 2200620498_63030816
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- [ ] 2200622355_63030956
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- [ ] 2200650089_63038093
- [ ] 2200666292_63076568
- [ ] 2200669188_63036688
- [ ] 2200669320_63040259
- [ ] 2200669383_63040254
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- [ ] 2200680342_63105271
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- [ ] 2200694789_63042862
- [ ] 2200694858_63042702
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- [ ] 2200699290_63043047
- [ ] 2200699345_63040238
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- [ ] 2200699412_63040731
- [ ] 220071551_63048935
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- [ ] 2200748171_63051213
- [ ] 2200751046_63051249
- [ ] 2200751101_63051234
- [ ] 2200766471_63054590
- [ ] 2200767731_63054595
- [ ] 2200767822_63054464
- [ ] 2200775505_63060410
- [ ] 2200850441_63019345
- [ ] 220597589_63026879
- [ ] 2300003253_63060430
- [ ] 2300005679_63060370
- [ ] 2300009914_63060390
- [ ] 2300028784_63060001
- [ ] 2300036815_63063357
- [ ] 2300055382_63061874
- [ ] 2300055421_63061871
- [ ] 2300055440_63061880
- [ ] 230006894_63064950
- [ ] 2300071111_63070356
- [ ] 2300083434_63071675
- [ ] 2300103609_63076239
- [ ] 2300104572_63076232
- [ ] 2300109602_63076765
- [ ] 2300109665_63076770
- [ ] 2300119721_63078732
- [ ] 2300137773_63078133
- [ ] 2300137834_63078123
- [ ] 2300167821_63086183
- [ ] 2300172698_63113453
- [ ] 2300188216_63090609
- [ ] 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
* Résultats
** TODO Speed-up BWA-mem
SCHEDULED: <2023-09-30 Sat>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-09-30 Sat>