apraga/org - Change FFRVLC5ETQ5C5VBU6RM26MGEHS76DMISRZMAOOTYDIIGAQVTWVYAC

Saving backup tasks

Created by Alexis Praga on October 1, 2023

FFRVLC5ETQ5C5VBU6RM26MGEHS76DMISRZMAOOTYDIIGAQVTWVYAC

Dependencies

In channels

main

Change contents

Replacement in projects.org at line 46 [5.123895]

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**** TODO Informations complémentaires Julien Thevenon
SCHEDULED: <2023-09-26 Tue>

[3.296]

[6.14]

**** DONE Informations complémentaires Julien Thevenon
CLOSED: [2023-10-01 Sun 14:49] SCHEDULED: <2023-09-26 Tue>

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B:BD[8.347] → [2.2756:2772]
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B:BD[8.416] → [2.2773:2786]
```
** TODO Tout avec git-annex
SCHEDULED: <2023-09-30 Sat>
*** TODO /annex
SCHEDULED: <2023-09-30 Sat>
- [ ] public
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[9.339]
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** TODO Git-annex en local
*** DONE vers /annex
CLOSED: [2023-10-01 Sun 15:34] SCHEDULED: <2023-09-30 Sat>
- [X] public
```

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- [ ] data
*** TODO raspberry:/media/annex
SCHEDULED: <2023-10-01 Sun>
- [ ] public

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- [X] data
*** DONE vers raspberry:/media/annex
CLOSED: [2023-10-01 Sun 15:34] SCHEDULED: <2023-10-01 Sun>
- [X] public

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- [ ] data
*** TODO laptop:~/annex
SCHEDULED: <2023-09-30 Sat>
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- [X] data
*** TODO vers laptop:~/annex
```

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*** TODO mega
SCHEDULED: <2023-10-01 Sun>
- [ ] public
- [ ] private

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*** DONE depuis /annex
CLOSED: [2023-10-01 Sun 16:15] SCHEDULED: <2023-09-30 Sat>
- [X] public
- [X] private

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*** TODO google drive
SCHEDULED: <2023-10-01 Sun>

[2.3026]

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*** TODO depuis raspberry:/media/annex
SCHEDULED: <2023-10-08 Sun>
À vérifier
- [X] public
- [X] private
- [ ] data
*** TODO depuis laptop:~/annex
SCHEDULED: <2023-10-08 Sun>

Insertion in projects.org at line 867 [5.123895]

[2.3116]

[9.474]

*** DONE mega avec restic
CLOSED: [2023-10-01 Sun 16:08] SCHEDULED: <2023-10-01 Sun>
- [X] public
- [X] private
*** DONE google drive avec restic
CLOSED: [2023-10-01 Sun 15:33] SCHEDULED: <2023-10-01 Sun>
- [X] public
- [X] private
*** DONE Tester backup avec restic
CLOSED: [2023-10-01 Sun 16:15] SCHEDULED: <2023-10-01 Sun>
- [X] private sur gdrive
- [ ] public sur gdrive

Replacement in projects/bisonex.org at line 28 [11.35]

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B:BD[12.8282] → [9.699:8860]

: <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
**** DONE Test sur 1 patient
CLOSED: [2023-09-30 Sat 23:54] 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: <2023-10-01 Sun>
/Entered on/ [2023-09-19 Tue 08:43]
** TODO Figure: nombre d'exomes par années
SCHEDULED: <2023-10-01 Sun>
/Entered on/ [2023-09-19 Tue 08:43]
* Tests :tests:
** KILL Non régression : version prod
CLOSED: [2023-05-23 Tue 08:46]
*** DONE ID common snp
CLOSED: [2022-11-19 Sat 21:36]
#+begin_src
$ wc -l ID_of_common_snp.txt
23194290 ID_of_common_snp.txt
$ wc -l /Work/Users/apraga/bisonex/database/dbSNP/ID_of_common_snp.txt
23194290 /Work/Users/apraga/bisonex/database/dbSNP/ID_of_common_snp.txt
#+end_src
*** DONE ID common snp not clinvar patho
CLOSED: [2022-12-11 Sun 20:11]
**** DONE Vérification du problème
CLOSED: [2022-12-11 Sun 16:30]
Sur le J:
21155134 /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt.ref
Version de "non-régression"
21155076 database/dbSNP/ID_of_common_snp_not_clinvar_patho.txt
Nouvelle version
23193391 /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt
Si on enlève les doublons
$ sort database/dbSNP/ID_of_common_snp_not_clinvar_patho.txt | uniq > old.txt
$ wc -l old.txt
21107097 old.txt
$ sort /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt | uniq > new.txt
$ wc -l new.txt
21174578 new.txt
$ sort /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt.ref | uniq > ref.txt
$ wc -l ref.txt
21107155 ref.txt
Si on regarde la différence
 comm -23 ref.txt old.txt
rs1052692
rs1057518973
rs1057518973
rs11074121
rs112848754
rs12573787
rs145033890
rs147889095
rs1553904159
rs1560294695
rs1560296615
rs1560310926
rs1560325547
rs1560342418
rs1560356225
rs1578287542
...
On cherche le premier
bcftools query -i 'ID="rs1052692"' database/dbSNP/dbSNP_common.vcf.gz -f '%CHROM %POS %REF %ALT\n'
NC_000019.10 1619351 C A,T
Il est bien patho...
$ bcftools query -i 'POS=1619351' database/clinvar/clinvar.vcf.gz -f '%CHROM %POS %REF %ALT %INFO/CLNSIG\n'
19 1619351 C T Conflicting_interpretations_of_pathogenicity
On vérifie pour tous les autres
$ comm -23 ref.txt old.txt > tocheck.txt
On génère les régions à vérifier (chromosome number:position)
$ bcftools query -i 'ID=@tocheck.txt' database/dbSNP/dbSNP_common.vcf.gz -f '%CHROM\t%POS\n' > tocheck.pos
On génère le mapping inverse (chromosome number -> NC)
$ awk ' { t = $1; $1 = $2; $2 = t; print; } ' database/RefSeq/refseq_to_number_only_consensual.txt  > mapping.txt
On remap clinvar
$ bcftools annotate --rename-chrs mapping.txt database/clinvar/clinvar.vcf.gz -o clinvar_remapped.vcf.gz
$ tabix clinvar_remapped.vcf.gz
Enfin, on cherche dans clinvar la classification
$ bcftools query -R tocheck.pos clinvar_remapped.vcf.gz -f '%CHROM %POS %INFO/CLNSIG\n'
$ bcftools query -R tocheck.pos database/dbSNP/dbSNP_common.vcf.gz -f '%CHROM %POS %ID \n' | grep '^NC'
#+RESULTS:
**** DONE Comprendre pourquoi la nouvelle version donne un résultat différent
CLOSED: [2022-12-11 Sun 20:11]
***** DONE Même version dbsnp et clinvar ?
CLOSED: [2022-12-10 Sat 23:02]
Clinvar différent !
  $ bcftools stats clinvar.gz
  clinvar (Alexis)
SN	0	number of samples:	0
SN	0	number of records:	1492828
SN	0	number of no-ALTs:	965
SN	0	number of SNPs:	1338007
SN	0	number of MNPs:	5562
SN	0	number of indels:	144580
SN	0	number of others:	3714
SN	0	number of multiallelic sites:	0
SN	0	number of multiallelic SNP sites:	0
clinvar (new)
SN	0	number of samples:	0
SN	0	number of records:	1493470
SN	0	number of no-ALTs:	965
SN	0	number of SNPs:	1338561
SN	0	number of MNPs:	5565
SN	0	number of indels:	144663
SN	0	number of others:	3716
SN	0	number of multiallelic sites:	0
SN	0	number of multiallelic SNP sites:	0
***** DONE Mettre à jour clinvar et dbnSNP pour travailler sur les mêm bases
CLOSED: [2022-12-11 Sun 12:10]
Problème persiste
***** DONE Supprimer la conversion en int du chromosome
CLOSED: [2022-12-10 Sat 19:29]
***** KILL Même NC ?
CLOSED: [2022-12-10 Sat 19:29]
$  zgrep "contig=<ID=NC_\(.*\)" clinvar/GRCh38/clinvar.vcf.gz > contig.clinvar
$ diff contig.txt contig.clinvar
< ##contig=<ID=NC_012920.1>
***** DONE Tester sur chromosome 19: ok
CLOSED: [2022-12-11 Sun 13:53]
On prépare les données
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
bcftools filter -i 'CHROM="NC_000019.10"' /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/dbSNP_common.vcf.gz -o dbSNP_common_19.vcf.gz
bcftools filter -i 'CHROM="NC_000019.10"' /Work/Groups/bisonex/data/clinvar/GRCh38/clinvar.vcf.gz -o clinvar_19.vcf.gz
bcftools filter -i 'CHROM="NC_000019.10"' /Work/Groups/bisonex/data-alexis/dbSNP/dbSNP_common.vcf.gz -o dbSNP_common_19_old.vcf.gz
 bcftools filter -i 'CHROM="19"' /Work/Groups/bisonex/data-alexis/clinvar/clinvar.vcf.gz -o clinvar_19_old.vcf.gz
#+end_src
On récupère les 2 versions du script
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
git checkout regression ../../script/pythonScript/clinvar_sbSNP.py
cp ../../script/pythonScript/clinvar_sbSNP.py clinvar_sbSNP_old.py
git checkout HEAD ../../script/pythonScript/clinvar_sbSNP.py
#+end_src
#+RESULTS:
On compare
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
python ../../script/pythonScript/clinvar_sbSNP.py clinvar_sbSNP.py --clinvar clinvar_19.vcf.gz --dbSNP dbSNP_common_19.vcf.gz --output tmp.txt
sort tmp.txt | uniq > new.txt
table=/Work/Groups/bisonex/data-alexis/RefSeq/refseq_to_number_only_consensual.txt
python clinvar_sbSNP_old.py --clinvar clinvar_19_old.vcf.gz --dbSNP dbSNP_common_19_old.vcf.gz --output tmp_old.txt --chrm_name_table $table
sort tmp_old.txt | uniq > old.txt
wc -l old.txt new.txt
#+end_src
#+RESULTS:
|  535155 | old.txt |
|  535194 | new.txt |
| 1070349 | total   |
Si on prend le premier manquant dans new, il est conflicting patho donc il ne devrait pas y être...
$ bcftools query -i 'ID="rs10418277"' dbSNP
_common_19.vcf.gz  -f '%CHROM %POS %REF %ALT\n'
NC_000019.10 54939682 C G,T
$ bcftools query -i 'ID="rs10418277"' dbSNP_common_19_old.vcf.gz  -f '%CHROM %POS %REF %ALT\n'
NC_000019.10 54939682 C G,T
$ bcftools query -i 'POS=54939682' clinvar_19.vcf.gz  -f '%POS %REF %ALT %INFO/CLNSIG\n'
54939682 C G Conflicting_interpretations_of_pathogenicity
54939682 C T Benign
$ bcftools query -i 'POS=54939682' clinvar_19_old.vcf.gz  -f '%POS %REF %ALT %INFO/CLNSIG\n'
54939682 C G Conflicting_interpretations_of_pathogenicity
54939682 C T Benign
$ grep rs10418277 *.txt
new.txt:rs10418277
tmp.txt:rs10418277
Le problème venait de la POS qui n'était plus convertie en int (suppression de la ligne par erreur ??)
On vérifie
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
python ../../script/pythonScript/clinvar_sbSNP.py --clinvar clinvar_19.vcf.gz --dbSNP dbSNP_common_19.vcf.gz --output tmp.txt
sort tmp.txt | uniq > new.txt
table=/Work/Groups/bisonex/data-alexis/RefSeq/refseq_to_number_only_consensual.txt
python clinvar_sbSNP_old.py --clinvar clinvar_19_old.vcf.gz --dbSNP dbSNP_common_19_old.vcf.gz --output tmp_old.txt --chrm_name_table $table
sort tmp_old.txt | uniq > old.txt
wc -l old.txt new.txt
diff old.txt new.txt
#+end_src
#+RESULTS:
|  535155 | old.txt |
|  535155 | new.txt |
| 1070310 | total   |
***** DONE Tester sur chromosome 19 et 20: ok
CLOSED: [2022-12-11 Sun 15:56]
On prépare les données
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
bcftools filter -i 'CHROM="NC_000019.10" | CHROM="NC_000020.11"' /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/dbSNP_common.vcf.gz -

[10.40959]

[9.8860]

: <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
*** DONE Ajouter gnomAD v3 :gnomadv3:
CLOSED: [2023-10-01 Sun 15:34] 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
**** DONE Test sur 1 patient
CLOSED: [2023-09-30 Sat 23:54] SCHEDULED: <2023-09-29 Fri>
**** DONE Reprendre run batch
CLOSED: [2023-10-01 Sun 15:34]
** 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: <2023-10-03 Tue>
/Entered on/ [2023-09-19 Tue 08:43]
** TODO Figure: nombre d'exomes par années
SCHEDULED: <2023-10-03 Tue>
/Entered on/ [2023-09-19 Tue 08:43]
* Tests :tests:
** KILL Non régression : version prod
CLOSED: [2023-05-23 Tue 08:46]
*** DONE ID common snp
CLOSED: [2022-11-19 Sat 21:36]
#+begin_src
$ wc -l ID_of_common_snp.txt
23194290 ID_of_common_snp.txt
$ wc -l /Work/Users/apraga/bisonex/database/dbSNP/ID_of_common_snp.txt
23194290 /Work/Users/apraga/bisonex/database/dbSNP/ID_of_common_snp.txt
#+end_src
*** DONE ID common snp not clinvar patho
CLOSED: [2022-12-11 Sun 20:11]
**** DONE Vérification du problème
CLOSED: [2022-12-11 Sun 16:30]
Sur le J:
21155134 /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt.ref
Version de "non-régression"
21155076 database/dbSNP/ID_of_common_snp_not_clinvar_patho.txt
Nouvelle version
23193391 /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt
Si on enlève les doublons
$ sort database/dbSNP/ID_of_common_snp_not_clinvar_patho.txt | uniq > old.txt
$ wc -l old.txt
21107097 old.txt
$ sort /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt | uniq > new.txt
$ wc -l new.txt
21174578 new.txt
$ sort /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/ID_of_common_snp_not_clinvar_patho.txt.ref | uniq > ref.txt
$ wc -l ref.txt
21107155 ref.txt
Si on regarde la différence
 comm -23 ref.txt old.txt
rs1052692
rs1057518973
rs1057518973
rs11074121
rs112848754
rs12573787
rs145033890
rs147889095
rs1553904159
rs1560294695
rs1560296615
rs1560310926
rs1560325547
rs1560342418
rs1560356225
rs1578287542
...
On cherche le premier
bcftools query -i 'ID="rs1052692"' database/dbSNP/dbSNP_common.vcf.gz -f '%CHROM %POS %REF %ALT\n'
NC_000019.10 1619351 C A,T
Il est bien patho...
$ bcftools query -i 'POS=1619351' database/clinvar/clinvar.vcf.gz -f '%CHROM %POS %REF %ALT %INFO/CLNSIG\n'
19 1619351 C T Conflicting_interpretations_of_pathogenicity
On vérifie pour tous les autres
$ comm -23 ref.txt old.txt > tocheck.txt
On génère les régions à vérifier (chromosome number:position)
$ bcftools query -i 'ID=@tocheck.txt' database/dbSNP/dbSNP_common.vcf.gz -f '%CHROM\t%POS\n' > tocheck.pos
On génère le mapping inverse (chromosome number -> NC)
$ awk ' { t = $1; $1 = $2; $2 = t; print; } ' database/RefSeq/refseq_to_number_only_consensual.txt  > mapping.txt
On remap clinvar
$ bcftools annotate --rename-chrs mapping.txt database/clinvar/clinvar.vcf.gz -o clinvar_remapped.vcf.gz
$ tabix clinvar_remapped.vcf.gz
Enfin, on cherche dans clinvar la classification
$ bcftools query -R tocheck.pos clinvar_remapped.vcf.gz -f '%CHROM %POS %INFO/CLNSIG\n'
$ bcftools query -R tocheck.pos database/dbSNP/dbSNP_common.vcf.gz -f '%CHROM %POS %ID \n' | grep '^NC'
#+RESULTS:
**** DONE Comprendre pourquoi la nouvelle version donne un résultat différent
CLOSED: [2022-12-11 Sun 20:11]
***** DONE Même version dbsnp et clinvar ?
CLOSED: [2022-12-10 Sat 23:02]
Clinvar différent !
  $ bcftools stats clinvar.gz
  clinvar (Alexis)
SN	0	number of samples:	0
SN	0	number of records:	1492828
SN	0	number of no-ALTs:	965
SN	0	number of SNPs:	1338007
SN	0	number of MNPs:	5562
SN	0	number of indels:	144580
SN	0	number of others:	3714
SN	0	number of multiallelic sites:	0
SN	0	number of multiallelic SNP sites:	0
clinvar (new)
SN	0	number of samples:	0
SN	0	number of records:	1493470
SN	0	number of no-ALTs:	965
SN	0	number of SNPs:	1338561
SN	0	number of MNPs:	5565
SN	0	number of indels:	144663
SN	0	number of others:	3716
SN	0	number of multiallelic sites:	0
SN	0	number of multiallelic SNP sites:	0
***** DONE Mettre à jour clinvar et dbnSNP pour travailler sur les mêm bases
CLOSED: [2022-12-11 Sun 12:10]
Problème persiste
***** DONE Supprimer la conversion en int du chromosome
CLOSED: [2022-12-10 Sat 19:29]
***** KILL Même NC ?
CLOSED: [2022-12-10 Sat 19:29]
$  zgrep "contig=<ID=NC_\(.*\)" clinvar/GRCh38/clinvar.vcf.gz > contig.clinvar
$ diff contig.txt contig.clinvar
< ##contig=<ID=NC_012920.1>
***** DONE Tester sur chromosome 19: ok
CLOSED: [2022-12-11 Sun 13:53]
On prépare les données
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
bcftools filter -i 'CHROM="NC_000019.10"' /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/dbSNP_common.vcf.gz -o dbSNP_common_19.vcf.gz
bcftools filter -i 'CHROM="NC_000019.10"' /Work/Groups/bisonex/data/clinvar/GRCh38/clinvar.vcf.gz -o clinvar_19.vcf.gz
bcftools filter -i 'CHROM="NC_000019.10"' /Work/Groups/bisonex/data-alexis/dbSNP/dbSNP_common.vcf.gz -o dbSNP_common_19_old.vcf.gz
 bcftools filter -i 'CHROM="19"' /Work/Groups/bisonex/data-alexis/clinvar/clinvar.vcf.gz -o clinvar_19_old.vcf.gz
#+end_src
On récupère les 2 versions du script
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
git checkout regression ../../script/pythonScript/clinvar_sbSNP.py
cp ../../script/pythonScript/clinvar_sbSNP.py clinvar_sbSNP_old.py
git checkout HEAD ../../script/pythonScript/clinvar_sbSNP.py
#+end_src
#+RESULTS:
On compare
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
python ../../script/pythonScript/clinvar_sbSNP.py clinvar_sbSNP.py --clinvar clinvar_19.vcf.gz --dbSNP dbSNP_common_19.vcf.gz --output tmp.txt
sort tmp.txt | uniq > new.txt
table=/Work/Groups/bisonex/data-alexis/RefSeq/refseq_to_number_only_consensual.txt
python clinvar_sbSNP_old.py --clinvar clinvar_19_old.vcf.gz --dbSNP dbSNP_common_19_old.vcf.gz --output tmp_old.txt --chrm_name_table $table
sort tmp_old.txt | uniq > old.txt
wc -l old.txt new.txt
#+end_src
#+RESULTS:
|  535155 | old.txt |
|  535194 | new.txt |
| 1070349 | total   |
Si on prend le premier manquant dans new, il est conflicting patho donc il ne devrait pas y être...
$ bcftools query -i 'ID="rs10418277"' dbSNP
_common_19.vcf.gz  -f '%CHROM %POS %REF %ALT\n'
NC_000019.10 54939682 C G,T
$ bcftools query -i 'ID="rs10418277"' dbSNP_common_19_old.vcf.gz  -f '%CHROM %POS %REF %ALT\n'
NC_000019.10 54939682 C G,T
$ bcftools query -i 'POS=54939682' clinvar_19.vcf.gz  -f '%POS %REF %ALT %INFO/CLNSIG\n'
54939682 C G Conflicting_interpretations_of_pathogenicity
54939682 C T Benign
$ bcftools query -i 'POS=54939682' clinvar_19_old.vcf.gz  -f '%POS %REF %ALT %INFO/CLNSIG\n'
54939682 C G Conflicting_interpretations_of_pathogenicity
54939682 C T Benign
$ grep rs10418277 *.txt
new.txt:rs10418277
tmp.txt:rs10418277
Le problème venait de la POS qui n'était plus convertie en int (suppression de la ligne par erreur ??)
On vérifie
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
python ../../script/pythonScript/clinvar_sbSNP.py --clinvar clinvar_19.vcf.gz --dbSNP dbSNP_common_19.vcf.gz --output tmp.txt
sort tmp.txt | uniq > new.txt
table=/Work/Groups/bisonex/data-alexis/RefSeq/refseq_to_number_only_consensual.txt
python clinvar_sbSNP_old.py --clinvar clinvar_19_old.vcf.gz --dbSNP dbSNP_common_19_old.vcf.gz --output tmp_old.txt --chrm_name_table $table
sort tmp_old.txt | uniq > old.txt
wc -l old.txt new.txt
diff old.txt new.txt
#+end_src
#+RESULTS:
|  535155 | old.txt |
|  535155 | new.txt |
| 1070310 | total   |
***** DONE Tester sur chromosome 19 et 20: ok
CLOSED: [2022-12-11 Sun 15:56]
On prépare les données
#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/debug-commonsnp
PATH=$PATH:$HOME/.nix-profile/bin
bcftools filter -i 'CHROM="NC_000019.10" | CHROM="NC_000020.11"' /Work/Groups/bisonex/data/dbSNP/GRCh38.p13/dbSNP_common.vcf.gz -

Replacement in projects/bisonex.org at line 77 [11.35]

B:BD[13.40315] → [13.40315:40346]

B:BD[13.40346] → [9.8892:16579]

te simplement REF et ALT avec a
nnotateLifted.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
** PROJ Lancer tests sur données brutes [108/250]
- [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
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- [ ] 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: <2023-10-01 Sun>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-10-01 Sun>

[13.40315]

te 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
** PROJ Lancer tests sur données brutes [108/250]
- [X] 100222_63015289
- [X] 1600304839_63051311
- [X] 1900007827_62913191
- [X] 1900398899_62999500
- [X] 1900486799_62913197
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- [ ] 2200650089_63038093
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- [ ] 2200669188_63036688
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- [ ] 2200699290_63043047
- [ ] 2200699345_63040238
- [ ] 2200699383_63043050
- [ ] 2200699412_63040731
- [ ] 220071551_63048935
- [ ] 2200731515_63048963
- [ ] 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
- [ ] 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: <2023-10-08 Sun>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-10-08 Sun>

Replacement in notes/20230930161424-backup.org at line 7 [8.46554]

B:BD[2.11558] → [2.11558:11747]

* Nouvelle version : git-annex sur plusieurs dépôts
** Discussion
Inconvénients
- git-annex est très lent pour de multiples fichiers
- il archive mais ne fait pas de vraies sauvegardes

[2.11558]

[2.11747]

* Nouvelle version : git-annex sur plusieurs dépôts + restic sur le cloud
Inconvénients de git-annex:
- très très lent pour de multiples fichiers sur google drive/mega (> 6h pour copier la moitié de public)
- archive mais ne fait pas de vraies sauvegardes

Replacement in notes/20230930161424-backup.org at line 12 [8.46554]
B:BD[2.11879] → [2.11879:11897]
```
- non encrypté ?
```
[2.11879]
[2.11897]
```
- encryption=hybrid ne marche pas
```

Insertion in notes/20230930161424-backup.org at line 20 [8.46554]

[2.12291]

[8.46659]

Conclusion
- git-annex pour les disque durs locaux
- sauvegarde avec restic sur google drive/mega
- Attention, pour que restic prennent les symlink dans la sauvegarde, on fait plusieurs dépoots

Deletion in notes/20230930161424-backup.org at line 25 [8.46554]

B:BD[8.46660] → [2.12292:12520]

On utilise encryption=shared pour mega et github : il suffit de cloner le sdépôt pour avoir accès à la clé (dans remote.log sur la branch git-annex). Inconvénient: ne pas la ma ttre sur github...
Clé stockée dans proton

Replacement in notes/20230930161424-backup.org at line 26 [8.46554]

B:BD[2.12521] → [2.12521:12569]

Encrpption=hybrid ne fonctionne pas avec gpg...

[2.12521]

[2.12569]

| Repo    | Taille | Archivage |                |                        | Sauvegarde   |      |
|         |   (Gb) | /annex    | laptop:~/annex | raspberry:/media/annex | drive | Mega |
|---------+--------+-----------+----------------+------------------------+--------------+------|
| papers  |        | oui       | oui            | oui                    |              |      |
| public  |      8 | oui       | oui            | oui                    | oui          | oui  |
| private |    0.8 | oui       | oui            | oui                    | oui          | oui  |
| data    |        | oui       | oui            | oui                    |              |      |
|         |        |           |                |                        |              |      |

Deletion in notes/20230930161424-backup.org at line 35 [8.46554]

B:BD[2.12570] → [2.12570:13216]

| Repo    | Taille | Crypté       | Mega | Google Drive | /annex | ~/annex    | Raspberry |
|         | (Gb)   |              |      |              | (tour) | (portable) |           |
|---------+--------+--------------+------+--------------+--------+------------+-----------|
| papers  |        | non          |      |              |        |            |           |
| public  |        | non          | oui  | oui          | oui    | oui        | oui       |
| private | 0.8    | oui (shared) | oui  | oui          | oui    | oui        | oui       |
| data    |        | non          |      |              | oui    | oui        | oui       |

Replacement in notes/20230930161424-backup.org at line 37 [8.46554]
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```
** Archivage
```
[8.46750]
[2.13255]
```
** Maintenance
```
Insertion in notes/20230930161424-backup.org at line 39 [8.46554]
[2.13275]
[9.18993]
```
#+begin_src nu
rsync -avz raspberry:Downloads/torrents private/
```

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#+begin_src sh
git annex sync --content

[9.18994]

[2.13316]

cd public ; git annex sync --content ; cd ..
cd private ; git annex sync --content ; cd ..
cd data ; git annex sync --content ; cd ..
$env.RESTIC_PASSWORD = (pass show Backup/restic-private)
restic -r rclone:gdrive:restic-private backup private
restic -r rclone:mega:restic-private backup private
$env.RESTIC_PASSWORD = (pass show Backup/restic-public)
restic -r rclone:gdrive:restic-public backup public
restic -r rclone:mega:restic-public backup public

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```
** Local
```
[2.13337]
[2.13346]
```
*** Archivage local
```
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B:BD[2.14010] → [2.14010:14039]
```
git annex sync zfs --content
```
[2.14010]
[2.14039]
```
git annex sync --content
```
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```
Idem pour raspberry
```
Replacement in notes/20230930161424-backup.org at line 124 [8.46554]
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```
Ne pas oubiler de le faire dans l'autre sens !
```
[9.20935]
[9.20935]
```
Ne pas oublier de le faire dans l'autre sens !
```

Insertion in notes/20230930161424-backup.org at line 131 [8.46554]

[9.20986]

[2.14173]

Idem pour private, data
*** Sauvegarde restic sur google drive et mega
Cf configuration rclone puis

Insertion in notes/20230930161424-backup.org at line 135 [8.46554]

[2.14174]

[8.46967]

#+begin_src nu
cd ~/annex
$env.RESTIC_PASSWORD = (pass show Backup/restic-private)
restic -r rclone:gdrive:restic-private init
restic -r rclone:mega:restic-private init
restic -r rclone:gdrive:restic-private backup private
restic -r rclone:mega:restic-private backup private
$env.RESTIC_PASSWORD = (pass show Backup/restic-public)
restic -r rclone:gdrive:restic-public init
restic -r rclone:mega:restic-public init
restic -r rclone:gdrive:restic-public backup public
restic -r rclone:mega:restic-public backup public
#+end_src

Replacement in notes/20230511181321-japonais.org at line 779 [5.353504]
B:BD[2.15370] → [2.15370:15388]
```
- ガスボンベ
```
[2.15370]
[2.15388]
```
- ガスボンベ: bouteille de gaz
```

Saving backup tasks

Dependencies

In channels

Change contents

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