B:BD[
6.15718] → [
2.352817:361009]
21:34]
*** DONE Haplotype caller
CLOSED: [2022-10-09 Sun 22:40]
*** DONE Filter variants
CLOSED: [2022-10-09 Sun 22:40]
*** DONE Filter common snp not clinvar path
CLOSED: [2022-11-07 Mon 23:00]
Voir [[*common dbSNP not clinvar patho][common dbSNP not clinvar patho]]
*** DONE Filter variant only in consensual sequence
CLOSED: [2022-11-08 Tue 22:23]
*** DONE Filter technical variants
CLOSED: [2022-11-19 Sat 21:34]
*** DONE Utilise AVX pour accélerer l'exécution
CLOSED: [2023-04-29 Sat 15:46]
Sans cela, on a l'avertissement
#+begin_quote
17:28:00.720 INFO PairHMM - OpenMP multi-threaded AVX-accelerated native PairHMM implementation is not supported
17:28:00.721 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/nix/store/cy9ckxqwrkifx7wf02hm4ww1p6lnbxg9-gatk-4.2.4.1/bin/gatk-package-4.2.4.1-local.jar!/com/intel/gkl/native/libgkl_utils.so
17:28:00.733 WARN NativeLibraryLoader - Unable to load libgkl_utils.so from native/libgkl_utils.so (/Work/Users/apraga/bisonex/out/NA12878_NIST7035/preprocessing/applybqsr/libgkl_utils821485189051585397.so: libgomp.so.1: cannot open shared object file: No such file or directory)
17:28:00.733 WARN IntelPairHmm - Intel GKL Utils not loaded
17:28:00.733 WARN PairHMM - ***WARNING: Machine does not have the AVX instruction set support needed for the accelerated AVX PairHmm. Falling back to the MUCH slower LOGLESS_CACHING implementation!
17:28:00.763 INFO ProgressMeter - Starting traversal
#+end_quote
libgomp.so est fourni par gcc donc il faut charger le module
module load gcc@11.3.0/gcc-12.1.0
** KILL Utiliser subworkflow
CLOSED: [2023-04-02 Sun 18:08]
Notre version permet d'être plus souple
*** KILL Alignement
CLOSED: [2023-04-02 Sun 18:08] SCHEDULED: <2023-04-05 Wed>
*** KILL Vep
CLOSED: [2023-04-02 Sun 18:08] SCHEDULED: <2023-04-05 Wed>
vcf_annotate_ensemblvep
** TODO Annotation avec nextflow :annotation:
*** KILL VEP : --gene-phenotype ?
CLOSED: [2023-04-18 mar. 18:32]
Vu avec alexis : bases de données non à jour
https://www.ensembl.org/info/genome/variation/phenotype/sources_phenotype_documentation.html
*** DONE plugin VEP
CLOSED: [2023-04-18 mar. 18:32]
Cloner dépôt git avec plugin
Puis utiliser --dir_plugins
*** HOLD Utiliser code d’Alexis
*** TODO Nouvelle version avec VEP
**** TODO Ajout spliceAI
SCHEDULED: <2023-04-30 Sun>
plugin VEP
**** TODO Ajout pLI
plugin VEP
**** KILL Ajout LOEUF
CLOSED: [2023-04-19 mer. 16:32]
plugin VEP
**** DONE Spip
CLOSED: [2023-05-01 Mon 23:07] SCHEDULED: <2023-04-30 Sun>
BED ne semble pas bien marcher (il faut définir une zone)
VCF : trop d’information
Attention, plusieurs transcripts mais résultats identiques. On supprimer les doublons
***** DONE interpretation + score + intervalle de confiance séparé
CLOSED: [2023-05-01 Mon 23:07] SCHEDULED: <2023-04-30 Sun>
Tests :
dans tests/
vep -i 63004925-small.vcf -o postvep.vcf --vcf --fasta genomeRef.fna --dir 109 --merged --pick --offline --custom ../script/spip_annotation.vcf.gz,SPIP,vcf,exact,0,spipInterp,spipScore,spipConfidence
***** DONE Score
CLOSED: [2023-04-22 Sat 15:30]
**** TODO CADD: remplacer par plugin VEP
***** Test
#+begin_src
vep -i test.vcf -o lol.vcf --offline --dir /Work/Projects/bisonex/data/vep/GRCh38/ --merged --vcf --fasta /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.fna --plugin CADD,/Work/Users/apraga/bisonex/work/13/9287a7fef17ab9365f5696f20710cd/gnomad.genomes.r3.0.snv.tsv.gz,/Work/Users/apraga/bisonex/work/13/9287a7fef17ab9365f5696f20710cd/gnomad.genomes.r3.0.indel.tsv.gz --dir_plugins ../VEP_plugins/ -v
#+end_src
Test
#+begin_src sh
vep --id "1 230710048 230710048 A/G 1" --offline --dir /Work/Projects/bisonex/data/vep/GRCh38/ --merged --vcf --fasta /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.fna --plugin CADD,/Work/Users/apraga/bisonex/work/13/9287a7fef17ab9365f5696f20710cd/gnomad.genomes.r3.0.snv.tsv.gz,/Work/Users/apraga/bisonex/work/13/9287a7fef17ab9365f5696f20710cd/gnomad.genomes.r3.0.indel.tsv.gz --hgvsg --plugin pLI --plugin LOEUF -o lol
#+end_src
CSQ=G|missense_variant|MODERATE|AGT|ENSG00000135744|Transcript|ENST00000366667|protein_coding|2/5||||843|776|259|M/T|aTg/aCg|||-1||HGNC|HGNC:333||Ensembl||A|A||1:g.230710048A>G|0.347|-0.277922|
Correspond bien à https://www.ensembl.org/Homo_sapiens/Tools/VEP/Results?tl=I7ZsIbrj14P6lD43-9115494
***** DONE Utiliser whole genome
CLOSED: [2023-04-29 Sat 15:46]
***** KILL Renommer les chromosome avant ...
CLOSED: [2023-05-01 Mon 09:14] SCHEDULED: <2023-04-30 Sun>
Trop long !
- Téléchargement de CADD: 4h20
- renommer les chromosome pour SNV : 6h20
- tabix sur les SNV : job tué au bout de 21h....
***** TODO annoter séparément et fusionner les tableaux
SCHEDULED: <2023-05-01 Mon>
NB: on pourrait filtrer CADD avec tabix pour se restreindre à nos variants
**** DONE clinvar
CLOSED: [2023-04-22 Sat 15:31]
**** STRT Remplacer script R par vep ?
Example avec --custom
https://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html
**** KILL Vérifier résultats HGVS avec mutalyzer
CLOSED: [2023-05-01 Mon 09:26]
**** TODO Parallélisation par chromosome avec workflow VEP
https://github.com/Ensembl/ensembl-vep/blob/release/109/nextflow/workflows/run_vep.nf
**** TODO OMIM
SCHEDULED: <2023-05-01 Mon>
**** TODO Grantham
SCHEDULED: <2023-05-01 Mon>
**** TODO ACMG incidental
SCHEDULED: <2023-05-01 Mon>
**** TODO Gnomad ?
SCHEDULED: <2023-05-01 Mon>
**** DONE Filtrer après VEP avec filter_vep
CLOSED: [2023-04-29 Sat 15:47]
nNon testé
*** HOLD Ancienne version
**** TODO HGVS
**** TODO Filtrer après VEP
**** TODO OMIM
**** TODO clinvar
**** TODO ACMG incidental
**** TODO Grantham
**** KILL LRG
CLOSED: [2023-04-18 mar. 17:22] SCHEDULED: <2023-04-18 Tue>
Vu avec alexis, n’est plus à jour
**** TODO Gnomad
** DONE Porter exactement la version d'Alexis sur Helios
CLOSED: [2023-01-14 Sat 17:56]
Branche "prod"
** STRT Tester version d'alexis avec Nix
*** 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]
*** TODO Filter
- [X] depth
- [ ] comon snp not path
Problème avec liste des ID
**** TODO variant annotation
Besoin de vep
*** TODO Variant calling
* Amélioration :amelioration:
* Documentation :doc:
** DONE Procédure d'installation nix + dependences pour VM CHU
CLOSED: [2023-04-22 Sat 15:27] SCHEDULED: <2023-04-13 Thu>
* Manuscript :manuscript:
* Tests :tests:
** WAIT Non régression : version prod
*** 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 %R
21:34]
*** DONE Haplotype caller
CLOSED: [2022-10-09 Sun 22:40]
*** DONE Filter variants
CLOSED: [2022-10-09 Sun 22:40]
*** DONE Filter common snp not clinvar path
CLOSED: [2022-11-07 Mon 23:00]
Voir [[*common dbSNP not clinvar patho][common dbSNP not clinvar patho]]
*** DONE Filter variant only in consensual sequence
CLOSED: [2022-11-08 Tue 22:23]
*** DONE Filter technical variants
CLOSED: [2022-11-19 Sat 21:34]
*** DONE Utilise AVX pour accélerer l'exécution
CLOSED: [2023-04-29 Sat 15:46]
Sans cela, on a l'avertissement
#+begin_quote
17:28:00.720 INFO PairHMM - OpenMP multi-threaded AVX-accelerated native PairHMM implementation is not supported
17:28:00.721 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/nix/store/cy9ckxqwrkifx7wf02hm4ww1p6lnbxg9-gatk-4.2.4.1/bin/gatk-package-4.2.4.1-local.jar!/com/intel/gkl/native/libgkl_utils.so
17:28:00.733 WARN NativeLibraryLoader - Unable to load libgkl_utils.so from native/libgkl_utils.so (/Work/Users/apraga/bisonex/out/NA12878_NIST7035/preprocessing/applybqsr/libgkl_utils821485189051585397.so: libgomp.so.1: cannot open shared object file: No such file or directory)
17:28:00.733 WARN IntelPairHmm - Intel GKL Utils not loaded
17:28:00.733 WARN PairHMM - ***WARNING: Machine does not have the AVX instruction set support needed for the accelerated AVX PairHmm. Falling back to the MUCH slower LOGLESS_CACHING implementation!
17:28:00.763 INFO ProgressMeter - Starting traversal
#+end_quote
libgomp.so est fourni par gcc donc il faut charger le module
module load gcc@11.3.0/gcc-12.1.0
** KILL Utiliser subworkflow
CLOSED: [2023-04-02 Sun 18:08]
Notre version permet d'être plus souple
*** KILL Alignement
CLOSED: [2023-04-02 Sun 18:08] SCHEDULED: <2023-04-05 Wed>
*** KILL Vep
CLOSED: [2023-04-02 Sun 18:08] SCHEDULED: <2023-04-05 Wed>
vcf_annotate_ensemblvep
** TODO Annotation avec nextflow :annotation:
*** KILL VEP : --gene-phenotype ?
CLOSED: [2023-04-18 mar. 18:32]
Vu avec alexis : bases de données non à jour
https://www.ensembl.org/info/genome/variation/phenotype/sources_phenotype_documentation.html
*** DONE plugin VEP
CLOSED: [2023-04-18 mar. 18:32]
Cloner dépôt git avec plugin
Puis utiliser --dir_plugins
*** HOLD Utiliser code d’Alexis
*** TODO Nouvelle version avec VEP
Example avec --custom
https://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html
**** TODO Ajout spliceAI
SCHEDULED: <2023-04-30 Sun>
plugin VEP
***** STRT Télécharger les données
Difficile d'automatiser, le lien est temporaire...
***** TODO PLugin
**** TODO Ajout pLI
plugin VEP
**** KILL Ajout LOEUF
CLOSED: [2023-04-19 mer. 16:32]
plugin VEP
**** DONE Spip
CLOSED: [2023-05-01 Mon 23:07] SCHEDULED: <2023-04-30 Sun>
BED ne semble pas bien marcher (il faut définir une zone)
VCF : trop d’information
Attention, plusieurs transcripts mais résultats identiques. On supprimer les doublons
***** DONE interpretation + score + intervalle de confiance séparé
CLOSED: [2023-05-01 Mon 23:07] SCHEDULED: <2023-04-30 Sun>
Tests :
dans tests/
vep -i 63004925-small.vcf -o postvep.vcf --vcf --fasta genomeRef.fna --dir 109 --merged --pick --offline --custom ../script/spip_annotation.vcf.gz,SPIP,vcf,exact,0,spipInterp,spipScore,spipConfidence
***** DONE Score
CLOSED: [2023-04-22 Sat 15:30]
**** DONE CADD: remplacer par plugin VEP
CLOSED: [2023-05-07 Sun 14:45] SCHEDULED: <2023-05-07 Sun>
***** Test
#+begin_src
vep -i test.vcf -o lol.vcf --offline --dir /Work/Projects/bisonex/data/vep/GRCh38/ --merged --vcf --fasta /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.fna --plugin CADD,/Work/Users/apraga/bisonex/work/13/9287a7fef17ab9365f5696f20710cd/gnomad.genomes.r3.0.snv.tsv.gz,/Work/Users/apraga/bisonex/work/13/9287a7fef17ab9365f5696f20710cd/gnomad.genomes.r3.0.indel.tsv.gz --dir_plugins ../VEP_plugins/ -v
#+end_src
Test
#+begin_src sh
vep --id "1 230710048 230710048 A/G 1" --offline --dir /Work/Projects/bisonex/data/vep/GRCh38/ --merged --vcf --fasta /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.fna --plugin CADD,/Work/Users/apraga/bisonex/work/13/9287a7fef17ab9365f5696f20710cd/gnomad.genomes.r3.0.snv.tsv.gz,/Work/Users/apraga/bisonex/work/13/9287a7fef17ab9365f5696f20710cd/gnomad.genomes.r3.0.indel.tsv.gz --hgvsg --plugin pLI --plugin LOEUF -o lol
#+end_src
CSQ=G|missense_variant|MODERATE|AGT|ENSG00000135744|Transcript|ENST00000366667|protein_coding|2/5||||843|776|259|M/T|aTg/aCg|||-1||HGNC|HGNC:333||Ensembl||A|A||1:g.230710048A>G|0.347|-0.277922|
Correspond bien à https://www.ensembl.org/Homo_sapiens/Tools/VEP/Results?tl=I7ZsIbrj14P6lD43-9115494
***** DONE Utiliser whole genome
CLOSED: [2023-04-29 Sat 15:46]
***** KILL Renommer les chromosome avant ...
CLOSED: [2023-05-01 Mon 09:14] SCHEDULED: <2023-04-30 Sun>
Trop long !
- Téléchargement de CADD: 4h20
- renommer les chromosome pour SNV : 6h20
- tabix sur les SNV : job tué au bout de 21h....
***** DONE annoter séparément et fusionner les tableaux
CLOSED: [2023-05-07 Sun 14:45] SCHEDULED: <2023-05-01 Mon>
NB: on pourrait filtrer CADD avec tabix pour se restreindre à nos variants
**** DONE clinvar
CLOSED: [2023-04-22 Sat 15:31]
**** KILL Vérifier résultats HGVS avec mutalyzer
CLOSED: [2023-05-01 Mon 09:26]
**** TODO Parallélisation
***** HOLD par chromosome avec workflow VEP
https://github.com/Ensembl/ensembl-vep/blob/release/109/nextflow/workflows/run_vep.nf
***** HOLD Avec option --fork
**** TODO Utiliser la version de nf-core de VEP
SCHEDULED: <2023-05-07 Sun>
**** DONE OMIM
CLOSED: [2023-05-08 Mon 15:02] SCHEDULED: <2023-05-01 Mon>
**** TODO Grantham
SCHEDULED: <2023-05-01 Mon>
**** TODO ACMG incidental
SCHEDULED: <2023-05-01 Mon>
**** TODO Gnomad ?
SCHEDULED: <2023-05-01 Mon>
**** DONE Filtrer après VEP avec filter_vep
CLOSED: [2023-04-29 Sat 15:47]
nNon testé
*** HOLD Ancienne version
**** TODO HGVS
**** TODO Filtrer après VEP
**** TODO OMIM
**** TODO clinvar
**** TODO ACMG incidental
**** TODO Grantham
**** KILL LRG
CLOSED: [2023-04-18 mar. 17:22] SCHEDULED: <2023-04-18 Tue>
Vu avec alexis, n’est plus à jour
**** TODO Gnomad
** DONE Porter exactement la version d'Alexis sur Helios
CLOSED: [2023-01-14 Sat 17:56]
Branche "prod"
** STRT Tester version d'alexis avec Nix
*** 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]
*** TODO Filter
- [X] depth
- [ ] comon snp not path
Problème avec liste des ID
**** TODO variant annotation
Besoin de vep
*** TODO Variant calling
* Amélioration :amelioration:
* Documentation :doc:
** DONE Procédure d'installation nix + dependences pour VM CHU
CLOSED: [2023-04-22 Sat 15:27] SCHEDULED: <2023-04-13 Thu>
* Manuscript :manuscript:
* Tests :tests:
** WAIT Non régression : version prod
*** 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 %R