644 | Acc | 0.0000003317384 | No | Acc | 89894637 | 7 | 89894644 | 0.0000002205815 | No | 89894637 | 0.02545572 | No | 0.02545572 | No |
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
**** DONE Vérifier multiples transcripts en hg38 avec coordonées génomiquues: ok
CLOSED: [2023-08-10 Thu 23:00]
Beaucoup plus de transcrits en T2T
Ex: 1 transcrit refseq curated
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr11%3A108257446%2D108257496&hgsid=1672963428_J5aWAqack2FpJ7mvhFTNVw7bKzxo
vs 2 transcrits en T2T
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hub_3671779_hs1&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr11%3A108264969%2D108265019&hgsid=1672963612_Eso9frdQ7z6RkKkcKsIf2Waq3pec
C'est bien ce qu'on retrouve avec spip
*** DONE [#A] Filtre vep avec spip
CLOSED: [2023-08-13 Sun 00:39] SCHEDULED: <2023-08-12 Sat 19:00>
*** DONE Annotation CADD + spliceAI GRCh38 avec nouvelle version :annotation:
CLOSED: [2023-08-28 Mon 17:21] SCHEDULED: <2023-08-20 Sun>
*** DONE OMIM: possible seulement sur nom du gènes:annotation:
CLOSED: [2023-08-13 Sun 11:57] SCHEDULED: <2023-08-13 Sun 16:00>
Base de données non disponible et compliqué de faire la mise à jour nous.
Si on essaie de prendre les gènes de GRCH38, ils ne sont pas forcément en T2T
Ex: DDX11L17 n'existe pas dans T2T à ces coordonées
zgrep DDX11L17 GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz
Note: c'est un pseudogene
https://www.genecards.org/cgi-bin/carddisp.pl?gene=DDX11L17
Si on prend les gènes de T2T, il y en a des nouveaux.
Ex: le premier est LOC101928626.
À cette position, rien en GRCh38
Si on essaye avec ENSEMBL: non car n'ont pas le même identifiant
Ex: ACHE
Idéalement, il faudrait l'identifiant NCBI (disponible dans OMIM) mais n'est pas en sortie de VEP
Et cela demande la version "merged" donc impossible en T2T
Est-ce faisable de faire une chr10129957338-T-Ccorrespondance sur le nom du gène ?
Tous les gènes de T2T:
#+begin_src sh :dir ~/Downloads
zgrep -o "ID=gene[^;]*;" GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz | sed 's/ID=gene-//;s/;//' | sort | uniq > t2t-genes.txt
wc -l t2t-genes.txt
#+end_src
#+RESULTS:
: 57660 t2t-genes.txt
#+begin_src sh :dir ~/Downloads
zgrep -o "ID=gene[^;]*;" GCF_000001405.40_GRCh38.p14_genomic.gff.gz | sed 's/ID=gene-//;s/;//' | sort | uniq > hg38-genes.txt
wc -l hg38-genes.txt
#+end_src
#+RESULTS:
: 67127 hg38-genes.txt
Gènes communs aux 2
#+begin_src sh :dir ~/Downloads
comm -12 t2t-genes.txt hg38-genes.txt | wc -l
#+end_src
#+RESULTS:
: 54506
Gènes uniquements dans t2t
#+begin_src sh :dir ~/Downloads
comm -
23 t2t-genes.txt hg38-genes.txt | wc -l
#+end_src
#+RESULTS:
: 3154
Gènes uniquements dans GRCh38
#+begin_src sh :dir ~/Downloads
comm -13 t2t-genes.txt hg38-genes.txt | wc -l
#+end_src
#+RESULTS:
: 12621
*** HOLD OMIM sur nom du gène :annotation:
*** DONE Mobidetails API
CLOSED: [2023-09-10 Sun 16:44]
Trop long ... 1h à 1h30 d'exécution
Disponible dans module
*** DONE Filtre vep avec spip for T2T et spliceAI pour GRCh38
CLOSED: [2023-09-16 Sat 22:47]
*** DONE Repasser tests en GRCh38 avec nouveau filtre (spip ou splice ai) :sanger:
CLOSED: [2023-09-17 Sun 09:07] SCHEDULED: <2023-09-16 Sat>
*** HOLD Franklin API
https://www.postman.com/genoox-ps/workspace/franklin-api-documentation-s-public-workspace/documentation/6621518-4335389d-12e3-445f-8182-339df95b2a09
*** KILL Regarder si clinique disponible avec vep :annotation:
CLOSED: [2023-09-10 Sun 16:44]
*** DONE Tester filtre sans splice: 6130 mais il en manque 4
CLOSED: [2023-09-28 Thu 01:33] SCHEDULED: <2023-09-27 Wed>
Mail Paul: Exome donc hors splice, peu intéressant
**** DONE Enlever complètement condition splice: 6130 variants restants...
CLOSED: [2023-09-27 Wed 19:37] SCHEDULED: <2023-09-26 Tue>
Cf [[id:c9b2009a-503b-4561-94c6-29ae21a3188d][Filtre vep avec spliceAI: 37365 -> 6130]]
Dans tests/splicai
#+begin_src sh
filter_vep -i output-all-gpu.vcf --format vcf --filter " not(Consequence matches non_coding_transcript or Consequence matches stream or Consequence matches intergenic_variant or Consequence matches UTR or Consequence matches intron_variant or Consequence matches synonymous or BIOTYPE matches pseudogene or BIOTYPE matches misc_RNA)" --only_matched -o test.vcf
grep -c -v '^#' test.vcf
6130
#+end_src
**** DONE Remplacer par impact fonctionnel: peu d'impact : majorité = MODERATE
CLOSED: [2023-09-27 Wed 19:45] SCHEDULED: <2023-09-26 Tue>
filter_vep -i output-all-gpu-filtered.vcf --format vcf --filter "IMPACT is HIGH" --only_matched | grep -c -v '^#'
258
filter_vep -i output-all-gpu-filtered.vcf --format vcf --filter "IMPACT is LOW" --only_matched | grep -c -v '^#'
11
filter_vep -i output-all-gpu-filtered.vcf --format vcf --filter "IMPACT is MODERATE" --only_matched | grep -c -v '^#'
5824
**** DONE Regarder les conséquences pour tes les transcripts
CLOSED: [2023-09-27 Wed 21:04]
/Work/Users/apraga/bisonex/out/annotate/vep/NA12878-sanger-all-T2T
filter_vep -i NA12878-sanger-all-T2T.vep.vcf.gz --format vcf --filter " not(Consequence matches non_coding_transcript or Consequence matches stream or Consequence matches intergenic_variant or Consequence matches UTR or Consequence matches intron_variant or Consequence matches synonymous or BIOTYPE matches pseudogene or BIOTYPE matches misc_RNA)" --only_matched -o filtered.vcf
bcftools +split-vep filtered.vcf -f '%Consequence\n' -d | sort | uniq -c
94 coding_sequence_variant
13 coding_sequence_variant&NMD_transcript_variant
257 frameshift_variant
21 frameshift_variant&NMD_transcript_variant
2 frameshift_variant&splice_donor_region_variant
20 frameshift_variant&splice_region_variant
1 frameshift_variant&splice_region_variant&NMD_transcript_variant
1 incomplete_terminal_codon_variant&coding_sequence_variant
211 inframe_deletion
18 inframe_deletion&NMD_transcript_variant
6 inframe_deletion&splice_region_variant
242 inframe_insertion
22 inframe_insertion&NMD_transcript_variant
4 inframe_insertion&splice_region_variant
14689 missense_variant
1416 missense_variant&NMD_transcript_variant
6 missense_variant&splice_donor_5th_base_variant
374 missense_variant&splice_region_variant
34 missense_variant&splice_region_variant&NMD_transcript_variant
53 splice_acceptor_variant
11 splice_acceptor_variant&NMD_transcript_variant
79 splice_donor_variant
6 splice_donor_variant&NMD_transcript_variant
30 start_lost
5 start_lost&NMD_transcript_variant
135 stop_gained
13 stop_gained&frameshift_variant
3 stop_gained&frameshift_variant&NMD_transcript_variant
2 stop_gained&frameshift_variant&splice_region_variant
14 stop_gained&NMD_transcript_variant
5 stop_gained&splice_region_variant
2 stop_gained&splice_region_variant&NMD_transcript_variant
4 stop_lost
1 stop_lost&NMD_transcript_variant
9 stop_retained_variant
6 stop_retained_variant&NMD_transcript_variant
1 transcript_ablation
Idem tests/spliceai
bcftools +split-vep output-all-gpu-filtered.vcf -f '%Consequence\n' -d | sort | uniq -c
94 coding_sequence_variant
13 coding_sequence_variant&NMD_transcript_variant
257 frameshift_variant
21 frameshift_variant&NMD_transcript_variant
2 frameshift_variant&splice_donor_region_variant
20 frameshift_variant&splice_region_variant
1 frameshift_variant&splice_region_variant&NMD_transcript_variant
1 incomplete_terminal_codon_variant&coding_sequence_variant
211 inframe_deletion
18 inframe_deletion&NMD_transcript_variant
6 inframe_deletion&splice_region_variant
242 inframe_insertion
22 inframe_insertion&NMD_transcript_variant
4 inframe_insertion&splice_region_variant
14689 missense_variant
1416 missense_variant&NMD_transcript_variant
6 missense_variant&splice_donor_5th_base_variant
374 missense_variant&splice_region_variant
34 missense_variant&splice_region_variant&NMD_transcript_variant
53 splice_acceptor_variant
11 splice_acceptor_variant&NMD_transcript_variant
79 splice_donor_variant
6 splice_donor_variant&NMD_transcript_variant
30 start_lost
5 start_lost&NMD_transcript_variant
135 stop_gained
13 stop_gained&frameshift_variant
3 stop_gained&frameshift_variant&NMD_transcript_variant
2 stop_gained&frameshift_variant&splice_region_variant
14 stop_gained&NMD_transcript_variant
5 stop_gained&splice_region_variant
2 stop_gained&splice_region_variant&NMD_transcript_variant
4 stop_lost
1 stop_lost&NMD_transcript_variant
9 stop_retained_variant
6 stop_retained_variant&NMD_transcript_variant
1 transcript_ablation
**** DONE Regarder les conséquences pour -s worst
CLOSED: [2023-09-27 Wed 21:04]
/Work/Users/apraga/bisonex/out/annotate/vep/NA12878-sanger-all-T2T
Après filtre_vep sans splice
]$ bcftools +split-vep filtered.vcf -f '%Consequence\n' -d -s worst | sort | uniq -c
48 coding_sequence_variant
6 coding_sequence_variant&nmd_transcript_variant
121 frameshift_variant
9 frameshift_variant&nmd_transcript_variant
1 frameshift_variant&splice_donor_region_variant
9 frameshift_variant&splice_region_variant
79 inframe_deletion
3 inframe_deletion&nmd_transcript_variant
2 inframe_deletion&splice_region_variant
85 inframe_insertion
2 inframe_insertion&nmd_transcript_variant
1 inframe_insertion&splice_region_variant
5309 missense_variant
207 missense_variant&nmd_transcript_variant
3 missense_variant&splice_donor_5th_base_variant
110 missense_variant&splice_region_variant
9 missense_variant&splice_region_variant&nmd_transcript_variant
19 splice_acceptor_variant
1 splice_acceptor_variant&nmd_transcript_variant
21 splice_donor_variant
1 splice_donor_variant&nmd_transcript_variant
14 start_lost
44 stop_gained
4 stop_gained&frameshift_variant
2 stop_gained&frameshift_variant&splice_region_variant
3 stop_gained&nmd_transcript_variant
3 stop_gained&splice_region_variant
2 stop_gained&splice_region_variant&nmd_transcript_variant
2 stop_lost
1 stop_lost&nmd_transcript_variant
6 stop_retained_variant
2 s
top_retained_variant&nmd_transcript_variant
1 transcript_ablation
Dans tests/spliceai
$ bcftools +split-vep output-all-gpu-filtered.vcf -f '%Consequence\n' -s worst -d | sort | uniq -c
48 coding_sequence_variant
6 coding_sequence_variant&nmd_transcript_variant
121 frameshift_variant
9 frameshift_variant&nmd_transcript_variant
1 frameshift_variant&splice_donor_region_variant
9 frameshift_variant&splice_region_variant
79 inframe_deletion
3 inframe_deletion&nmd_transcript_variant
2 inframe_deletion&splice_region_variant
85 inframe_insertion
2 inframe_insertion&nmd_transcript_variant
1 inframe_insertion&splice_region_variant
5309 missense_variant
207 missense_variant&nmd_transcript_variant
3 missense_variant&splice_donor_5th_base_variant
110 missense_variant&splice_region_variant
9 missense_variant&splice_region_variant&nmd_transcript_variant
19 splice_acceptor_variant
1 splice_acceptor_variant&nmd_transcript_variant
21 splice_donor_variant
1 splice_donor_variant&nmd_transcript_variant
14 start_lost
44 stop_gained
4 stop_gained&frameshift_variant
2 stop_gained&frameshift_variant&splice_region_variant
3 stop_gained&nmd_transcript_variant
3 stop_gained&splice_region_variant
2 stop_gained&splice_region_variant&nmd_transcript_variant
2 stop_lost
1 stop_lost&nmd_transcript_variant
6 stop_retained_variant
2 stop_retained_variant&nmd_transcript_variant
1 transcript_ablation
**** KILL Vérifier si tests sanger passent: non
CLOSED: [2023-09-28 Thu 01:33] SCHEDULED: <2023-09-27 Wed>
│ String Float64 Int64
─────┼───────────────────────────────────────
1 │ chr10:g.130884530 60.0 67
2 │ chr10:g.240362 60.0 79
3 │ chr14:g.52665581 60.0 51
4 │ chr19:g.41325390 60.0 180
** DONE [#B] Indicateurs qualité :qualité:
CLOSED: [2023-09-10 Sun 16:46]
*** Idée
Raredisease:
- FastQC : nombreuses statistiques. Non disponible Nix
- Mosdepth : calcule la profondeur (2x plus rapide que samtools depth). Nix
- MultiQC : fusionne juste les résultats des analyses. Non disponible nix
- Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics
- Qualimap : alternative fastqc ? Non disponible nix
- Sentieon's WgsMetricsAlgo : propriétaire
- TIDDIT's cov : TIDIT = remaninement chromosomique
Sarek:
- alignment statistics : samtools stats, mosdepth
- QC : MultiQC
MultiQC : non disponible Nix
*** DONE FastqQC
CLOSED: [2023-08-15 Tue 21:43] SCHEDULED: <2023-08-13 Sun>
*** DONE Mosdepth
CLOSED: [2023-08-15 Tue 21:43] SCHEDULED: <2023-08-13 Sun>
Pour exomple, il faut le fichier de capture
subworkflows/local/bam_markduplicates/
*** DONE Samtools stats
CLOSED: [2023-08-15 Tue 21:43] SCHEDULED: <2023-08-13 Sun>
*** DONE [#B] Compte-redu exécution avec MultiQC
CLOSED: [2023-08-15 Tue 21:43] SCHEDULED: <2023-08-13 Sun>
*** DONE Résultats sur NA12878 : 98% à 20x
CLOSED: [2023-08-19 Sat 20:45] SCHEDULED: <2023-08-17 Thu>
**** DONE Comprendre 91% à 20x seulement: SNVs inséré
CLOSED: [2023-08-18 Fri 22:25]
***** DONE Tester autre kit : Twist exome comprehensive
CLOSED: [2023-08-18 Fri 22:24]
Moins bon
***** DONE Tester génome sans alt
CLOSED: [2023-08-18 Fri 22:25]
Idem
***** DONE Tester NA12878 sans SNVs inséré: cause !!
CLOSED: [2023-08-18 Fri 22:25]
***** DONE Tester hg19 sur NA12878 non inséré
CLOSED: [2023-08-18 Fri 22:25]
**** DONE Comprendre pourquoi SNVs diminuent le score: reads manquants
CLOSED: [2023-08-19 Sat 20:34] SCHEDULED: <2023-08-18 Fri>
Voir [[id:5c1c36f3-f68e-4e6d-a7b6-61dca89abc37][Bug: perte de nombreux reads avec NA12878]]
*** DONE Relancer résultats avec NA1287 et NA12878 + sanger
CLOSED: [2023-08-29 Tue 10:30] SCHEDULED: <2023-08-29 Tue>
*** DONE Comparer avec hg19
CLOSED: [2023-08-28 Mon 17:22] SCHEDULED: <2023-08-20 Sun>
*** DONE Comparer avec autres kit de capture
CLOSED: [2023-08-28 Mon 17:22] SCHEDULED: <2023-08-20 Sun>
*** DONE Comparer avec no-alt
CLOSED: [2023-08-28 Mon 17:22] SCHEDULED: <2023-08-20 Sun>
** HOLD vérifier si normalisation
** KILL [#B] Vérification nomenclature hgvs :hgvs:
CLOSED: [2023-08-16 Wed 19:07] SCHEDULED: <2023-08-15 Tue>
*** KILL mutalyzer
CLOSED: [2023-08-16 Wed 19:07] SCHEDULED: <2023-08-13 Sun>
*** KILL API variantvalidator
CLOSED: [2023-08-16 Wed 19:07] SCHEDULED: <2023-08-13 Sun>
** DO
644 | Acc | 0.0000003317384 | No | Acc | 89894637 | 7 | 89894644 | 0.0000002205815 | No | 89894637 | 0.02545572 | No | 0.02545572 | No |
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
**** DONE Vérifier multiples transcripts en hg38 avec coordonées génomiquues: ok
CLOSED: [2023-08-10 Thu 23:00]
Beaucoup plus de transcrits en T2T
Ex: 1 transcrit refseq curated
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr11%3A108257446%2D108257496&hgsid=1672963428_J5aWAqack2FpJ7mvhFTNVw7bKzxo
vs 2 transcrits en T2T
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hub_3671779_hs1&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr11%3A108264969%2D108265019&hgsid=1672963612_Eso9frdQ7z6RkKkcKsIf2Waq3pec
C'est bien ce qu'on retrouve avec spip
*** DONE [#A] Filtre vep avec spip
CLOSED: [2023-08-13 Sun 00:39] SCHEDULED: <2023-08-12 Sat 19:00>
*** DONE Annotation CADD + spliceAI GRCh38 avec nouvelle version :annotation:
CLOSED: [2023-08-28 Mon 17:21] SCHEDULED: <2023-08-20 Sun>
*** DONE OMIM: possible seulement sur nom du gènes:annotation:
CLOSED: [2023-08-13 Sun 11:57] SCHEDULED: <2023-08-13 Sun 16:00>
Base de données non disponible et compliqué de faire la mise à jour nous.
Si on essaie de prendre les gènes de GRCH38, ils ne sont pas forcément en T2T
Ex: DDX11L17 n'existe pas dans T2T à ces coordonées
zgrep DDX11L17 GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz
Note: c'est un pseudogene
https://www.genecards.org/cgi-bin/carddisp.pl?gene=DDX11L17
Si on prend les gènes de T2T, il y en a des nouveaux.
Ex: le premier est LOC101928626.
À cette position, rien en GRCh38
Si on essaye avec ENSEMBL: non car n'ont pas le même identifiant
Ex: ACHE
Idéalement, il faudrait l'identifiant NCBI (disponible dans OMIM) mais n'est pas en sortie de VEP
Et cela demande la version "merged" donc impossible en T2T
Est-ce faisable de faire une chr10129957338-T-Ccorrespondance sur le nom du gène ?
Tous les gènes de T2T:
#+begin_src sh :dir ~/Downloads
zgrep -o "ID=gene[^;]*;" GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz | sed 's/ID=gene-//;s/;//' | sort | uniq > t2t-genes.txt
wc -l t2t-genes.txt
#+end_src
#+RESULTS:
: 57660 t2t-genes.txt
#+begin_src sh :dir ~/Downloads
zgrep -o "ID=gene[^;]*;" GCF_000001405.40_GRCh38.p14_genomic.gff.gz | sed 's/ID=gene-//;s/;//' | sort | uniq > hg38-genes.txt
wc -l hg38-genes.txt
#+end_src
#+RESULTS:
: 67127 hg38-genes.txt
Gènes communs aux 2
#+begin_src sh :dir ~/Downloads
comm -12 t2t-genes.txt hg38-genes.txt | wc -l
#+end_src
#+RESULTS:
: 54506
Gènes uniquements dans t2t
#+begin_src sh :dir ~/Downloads
comm -23 t2t-genes.txt hg38-genes.txt | wc -l
#+end_src
#+RESULTS:
: 3154
Gènes uniquements dans GRCh38
#+begin_src sh :dir ~/Downloads
comm -13 t2t-genes.txt hg38-genes.txt | wc -l
#+end_src
#+RESULTS:
: 12621
*** HOLD OMIM sur nom du gène :annotation:
*** DONE Mobidetails API
CLOSED: [2023-09-10 Sun 16:44]
Trop long ... 1h à 1h30 d'exécution
Disponible dans module
*** DONE Filtre vep avec spip for T2T et spliceAI pour GRCh38
CLOSED: [2023-09-16 Sat 22:47]
*** DONE Repasser tests en GRCh38 avec nouveau filtre (spip ou splice ai) :sanger:
CLOSED: [2023-09-17 Sun 09:07] SCHEDULED: <2023-09-16 Sat>
*** HOLD Franklin API
https://www.postman.com/genoox-ps/workspace/franklin-api-documentation-s-public-workspace/documentation/6621518-4335389d-12e3-445f-8182-339df95b2a09
*** KILL Regarder si clinique disponible avec vep :annotation:
CLOSED: [2023-09-10 Sun 16:44]
*** TODO Tester filtre sans splice: 6130 mais il en manque 4
SCHEDULED: <2023-09-27 Wed>
Mail Paul: Exome donc hors splice, peu intéressant
**** DONE Enlever complètement condition splice: 6130 variants restants...
CLOSED: [2023-09-27 Wed 19:37] SCHEDULED: <2023-09-26 Tue>
Cf [[id:c9b2009a-503b-4561-94c6-29ae21a3188d][Filtre vep avec spliceAI: 37365 -> 6130]]
Dans tests/splicai
#+begin_src sh
filter_vep -i output-all-gpu.vcf --format vcf --filter " not(Consequence matches non_coding_transcript or Consequence matches stream or Consequence matches intergenic_variant or Consequence matches UTR or Consequence matches intron_variant or Consequence matches synonymous or BIOTYPE matches pseudogene or BIOTYPE matches misc_RNA)" --only_matched -o test.vcf
grep -c -v '^#' test.vcf
6130
#+end_src
**** DONE Remplacer par impact fonctionnel: peu d'impact : majorité = MODERATE
CLOSED: [2023-09-27 Wed 19:45] SCHEDULED: <2023-09-26 Tue>
filter_vep -i output-all-gpu-filtered.vcf --format vcf --filter "IMPACT is HIGH" --only_matched | grep -c -v '^#'
258
filter_vep -i output-all-gpu-filtered.vcf --format vcf --filter "IMPACT is LOW" --only_matched | grep -c -v '^#'
11
filter_vep -i output-all-gpu-filtered.vcf --format vcf --filter "IMPACT is MODERATE" --only_matched | grep -c -v '^#'
5824
**** DONE Regarder les conséquences pour tes les transcripts
CLOSED: [2023-09-27 Wed 21:04]
/Work/Users/apraga/bisonex/out/annotate/vep/NA12878-sanger-all-T2T
filter_vep -i NA12878-sanger-all-T2T.vep.vcf.gz --format vcf --filter " not(Consequence matches non_coding_transcript or Consequence matches stream or Consequence matches intergenic_variant or Consequence matches UTR or Consequence matches intron_variant or Consequence matches synonymous or BIOTYPE matches pseudogene or BIOTYPE matches misc_RNA)" --only_matched -o filtered.vcf
bcftools +split-vep filtered.vcf -f '%Consequence\n' -d | sort | uniq -c
94 coding_sequence_variant
13 coding_sequence_variant&NMD_transcript_variant
257 frameshift_variant
21 frameshift_variant&NMD_transcript_variant
2 frameshift_variant&splice_donor_region_variant
20 frameshift_variant&splice_region_variant
1 frameshift_variant&splice_region_variant&NMD_transcript_variant
1 incomplete_terminal_codon_variant&coding_sequence_variant
211 inframe_deletion
18 inframe_deletion&NMD_transcript_variant
6 inframe_deletion&splice_region_variant
242 inframe_insertion
22 inframe_insertion&NMD_transcript_variant
4 inframe_insertion&splice_region_variant
14689 missense_variant
1416 missense_variant&NMD_transcript_variant
6 missense_variant&splice_donor_5th_base_variant
374 missense_variant&splice_region_variant
34 missense_variant&splice_region_variant&NMD_transcript_variant
53 splice_acceptor_variant
11 splice_acceptor_variant&NMD_transcript_variant
79 splice_donor_variant
6 splice_donor_variant&NMD_transcript_variant
30 start_lost
5 start_lost&NMD_transcript_variant
135 stop_gained
13 stop_gained&frameshift_variant
3 stop_gained&frameshift_variant&NMD_transcript_variant
2 stop_gained&frameshift_variant&splice_region_variant
14 stop_gained&NMD_transcript_variant
5 stop_gained&splice_region_variant
2 stop_gained&splice_region_variant&NMD_transcript_variant
4 stop_lost
1 stop_lost&NMD_transcript_variant
9 stop_retained_variant
6 stop_retained_variant&NMD_transcript_variant
1 transcript_ablation
Idem tests/spliceai
bcftools +split-vep output-all-gpu-filtered.vcf -f '%Consequence\n' -d | sort | uniq -c
94 coding_sequence_variant
13 coding_sequence_variant&NMD_transcript_variant
257 frameshift_variant
21 frameshift_variant&NMD_transcript_variant
2 frameshift_variant&splice_donor_region_variant
20 frameshift_variant&splice_region_variant
1 frameshift_variant&splice_region_variant&NMD_transcript_variant
1 incomplete_terminal_codon_variant&coding_sequence_variant
211 inframe_deletion
18 inframe_deletion&NMD_transcript_variant
6 inframe_deletion&splice_region_variant
242 inframe_insertion
22 inframe_insertion&NMD_transcript_variant
4 inframe_insertion&splice_region_variant
14689 missense_variant
1416 missense_variant&NMD_transcript_variant
6 missense_variant&splice_donor_5th_base_variant
374 missense_variant&splice_region_variant
34 missense_variant&splice_region_variant&NMD_transcript_variant
53 splice_acceptor_variant
11 splice_acceptor_variant&NMD_transcript_variant
79 splice_donor_variant
6 splice_donor_variant&NMD_transcript_variant
30 start_lost
5 start_lost&NMD_transcript_variant
135 stop_gained
13 stop_gained&frameshift_variant
3 stop_gained&frameshift_variant&NMD_transcript_variant
2 stop_gained&frameshift_variant&splice_region_variant
14 stop_gained&NMD_transcript_variant
5 stop_gained&splice_region_variant
2 stop_gained&splice_region_variant&NMD_transcript_variant
4 stop_lost
1 stop_lost&NMD_transcript_variant
9 stop_retained_variant
6 stop_retained_variant&NMD_transcript_variant
1 transcript_ablation
**** DONE Regarder les conséquences pour -s worst
CLOSED: [2023-09-27 Wed 21:04]
/Work/Users/apraga/bisonex/out/annotate/vep/NA12878-sanger-all-T2T
Après filtre_vep sans splice
]$ bcftools +split-vep filtered.vcf -f '%Consequence\n' -d -s worst | sort | uniq -c
48 coding_sequence_variant
6 coding_sequence_variant&nmd_transcript_variant
121 frameshift_variant
9 frameshift_variant&nmd_transcript_variant
1 frameshift_variant&splice_donor_region_variant
9 frameshift_variant&splice_region_variant
79 inframe_deletion
3 inframe_deletion&nmd_transcript_variant
2 inframe_deletion&splice_region_variant
85 inframe_insertion
2 inframe_insertion&nmd_transcript_variant
1 inframe_insertion&splice_region_variant
5309 missense_variant
207 missense_variant&nmd_transcript_variant
3 missense_variant&splice_donor_5th_base_variant
110 missense_variant&splice_region_variant
9 missense_variant&splice_region_variant&nmd_transcript_variant
19 splice_acceptor_variant
1 splice_acceptor_variant&nmd_transcript_variant
21 splice_donor_variant
1 splice_donor_variant&nmd_transcript_variant
14 start_lost
44 stop_gained
4 stop_gained&frameshift_variant
2 stop_gained&frameshift_variant&splice_region_variant
3 stop_gained&nmd_transcript_variant
3 stop_gained&splice_region_variant
2 stop_gained&splice_region_variant&nmd_transcript_variant
2 stop_lost
1 stop_lost&nmd_transcript_variant
6 stop_retained_variant
2 stop_retained_variant&nmd_transcript_variant
1 transcript_ablation
Dans tests/spliceai
$ bcftools +split-vep output-all-gpu-filtered.vcf -f '%Consequence\n' -s worst -d | sort | uniq -c
48 coding_sequence_variant
6 coding_sequence_variant&nmd_transcript_variant
121 frameshift_variant
9 frameshift_variant&nmd_transcript_variant
1 frameshift_variant&splice_donor_region_variant
9 frameshift_variant&splice_region_variant
79 inframe_deletion
3 inframe_deletion&nmd_transcript_variant
2 inframe_deletion&splice_region_variant
85 inframe_insertion
2 inframe_insertion&nmd_transcript_variant
1 inframe_insertion&splice_region_variant
5309 missense_variant
207 missense_variant&nmd_transcript_variant
3 missense_variant&splice_donor_5th_base_variant
110 missense_variant&splice_region_variant
9 missense_variant&splice_region_variant&nmd_transcript_variant
19 splice_acceptor_variant
1 splice_acceptor_variant&nmd_transcript_variant
21 splice_donor_variant
1 splice_donor_variant&nmd_transcript_variant
14 start_lost
44 stop_gained
4 stop_gained&frameshift_variant
2 stop_gained&frameshift_variant&splice_region_variant
3 stop_gained&nmd_transcript_variant
3 stop_gained&splice_region_variant
2 stop_gained&splice_region_variant&nmd_transcript_variant
2 stop_lost
1 stop_lost&nmd_transcript_variant
6 stop_retained_variant
2 stop_retained_variant&nmd_transcript_variant
1 transcript_ablation
**** KILL Vérifier si tests sanger passent: non
CLOSED: [2023-09-28 Thu 01:33] SCHEDULED: <2023-09-27 Wed>
│ String Float64 Int64
─────┼───────────────────────────────────────
1 │ chr10:g.130884530 60.0 67
2 │ chr10:g.240362 60.0 79
3 │ chr14:g.52665581 60.0 51
4 │ chr19:g.41325390 60.0 180
**** DONE Comparer aux filtres en GRCh38: ce sont bien les filtres hors splice...
CLOSED: [2023-10-17 Tue 21:12]
T2T:
filter_vep -i 2300346867_NA12878-63118093_S260-T2T/2300346867_NA12878-63118093_S260-T2T.vep.vcf.gz --format vcf --filter " not(Consequence matches non_coding_transcript or Consequence matches stream or Consequence matches intergenic_variant or Consequence matches UTR or Consequence matches intron_variant or Consequence matches synonymous or BIOTYPE matches pseudogene or BIOTYPE matches misc_RNA)" --only_matched | bcftools +counts
Number of samples: 1
Number of SNPs: 5362
Number of INDELs: 325
Number of MNPs: 323
Number of others: 0
Number of sites: 5991
GRCh38
filter_vep -i 2300346867_NA12878-63118093_S260-GRCh38/2300346867_NA12878-63118093_S260-GRCh38.vep.vcf.gz --format vcf --filter " not(Consequence matches non_coding_transcript or Consequence matches stream or Consequence matches intergenic_variant or Consequence matches UTR or Consequence matches intron_variant or Consequence matches synonymous or BIOTYPE matches pseudogene or BIOTYPE matches misc_RNA)" --only_matched | bcftools +counts
Number of samples: 1
Number of SNPs: 1182
Number of INDELs: 143
Number of MNPs: 535
Number of others: 0
Number of sites: 1840
**** DONE Proportions de conséquence : T2T vs GRCh38 avec multiqc: idem
CLOSED: [2023-10-17 Tue 21:00]
À l'oeil
**** Réexaminer les conséquences
***** DONE Impact fonctionnel: plus de LOW et de MODIFIER++
CLOSED: [2023-10-17 Tue 21:22]
T2T
bcftools +split-vep 2300346867_NA12878-63118093_S260-T2T/2300346867_NA12878-63118093_S260-T2T.filtervep.vcf -f '%IMPACT\n' -d | sort | uniq -c
596 HIGH
2828 LOW
16314 MODERATE
11261 MODIFIER
GRCh38
bcftools +split-vep 2300346867_NA12878-63118093_S260-GRCh38/2300346867_NA12878-63118093_S260-GRCh38.filtervep.vcf -f '%IMPACT\n' -d | sort | uniq -c
414 HIGH
466 LOW
10054 MODERATE
550 MODIFIER
***** DONE Pire conséquence: trop de missense
CLOSED: [2023-10-17 Tue 21:23]
GRCh38
$ bcftools +split-vep 2300346867_NA12878-63118093_S260-GRCh38/2300346867_NA12878-63118093_S260-GRCh38.filtervep.vcf -f '%Consequence\n' -d -s worst | sort | uniq -c
2 3_prime_utr_variant&nmd_transcript_variant
1 5_prime_utr_variant
2 coding_sequence_variant
47 frameshift_variant
6 frameshift_variant&nmd_transcript_variant
1 frameshift_variant&splice_donor_region_variant
1 frameshift_variant&splice_region_variant
1 frameshift_variant&start_lost&start_retained_variant
37 inframe_deletion
9 inframe_deletion&nmd_transcript_variant
27 inframe_insertion
5 inframe_insertion&nmd_transcript_variant
21 intron_variant
1593 missense_variant
37 missense_variant&nmd_transcript_variant
17 missense_variant&splice_region_variant
1 missense_variant&splice_region_variant&nmd_transcript_variant
1 protein_altering_variant
1 splice_acceptor_variant
1 splice_acceptor_variant&frameshift_variant
2 splice_acceptor_variant&nmd_transcript_variant
3 splice_donor_5th_base_variant&intron_variant
1 splice_donor_5th_base_variant&intron_variant&non_coding_transcript_variant
2 splice_donor_region_variant&intron_variant
1 splice_donor_region_variant&intron_variant&nmd_transcript_variant
1 splice_donor_region_variant&intron_variant&non_coding_transcript_variant
10 splice_donor_variant
1 splice_donor_variant&non_coding_transcript_variant
11 splice_polypyrimidine_tract_variant&intron_variant
1 splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant
1 splice_region_variant&intron_variant
9 splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant
3 splice_region_variant&synonymous_variant
1 splice_region_variant&synonymous_variant&nmd_transcript_variant
4 start_lost
19 stop_gained
2 stop_gained&frameshift_variant
2 stop_gained&nmd_transcript_variant
1 stop_gained&splice_region_variant
1 stop_gained&splice_region_variant&nmd_transcript_variant
3 stop_lost
2 stop_lost&nmd_transcript_variant
1 stop_retained_variant
18 synonymous_variant
1 synonymous_variant&nmd_transcript_variant
1 transcript_ablation
T2T
[apraga@mesointeractive filter]$ bcftools +split-vep 2300346867_NA12878-63118093_S260-T2T/2300346867_NA12878-63118093_S260-T2T.filtervep.vcf -f '%Consequence\n' -d -s worst | sort | uniq -c
15 3_prime_utr_variant
11 3_prime_utr_variant&nmd_transcript_variant
51 5_prime_utr_variant
3 5_prime_utr_variant&nmd_transcript_variant
48 coding_sequence_variant
5 coding_sequence_variant&nmd_transcript_variant
3 downstream_gene_variant
121 frameshift_variant
9 frameshift_variant&nmd_transcript_variant
1 frameshift_variant&splice_donor_region_variant
9 frameshift_variant&splice_region_variant
78 inframe_deletion
2 inframe_deletion&nmd_transcript_variant
2 inframe_deletion&splice_region_variant
84 inframe_insertion
2 inframe_insertion&nmd_transcript_variant
1 inframe_insertion&splice_region_variant
16 intergenic_variant
368 intron_variant
21 intron_variant&nmd_transcript_variant
71 intron_variant&non_coding_transcript_variant
5187 missense_variant
207 missense_variant&nmd_transcript_variant
3 missense_variant&splice_donor_5th_base_variant
105 missense_variant&splice_region_variant
9 missense_variant&splice_region_variant&nmd_transcript_variant
33 non_coding_transcript_exon_variant
12 splice_acceptor_variant
1 splice_acceptor_variant&5_prime_utr_variant&intron_variant&nmd_transcript_variant
1 splice_acceptor_variant&nmd_transcript_variant
3 splice_acceptor_variant&non_coding_transcript_variant
1 splice_acceptor_variant&splice_polypyrimidine_tract_variant&intron_variant&nmd_transcript_variant
16 splice_donor_5th_base_variant&intron_variant
2 splice_donor_5th_base_variant&intron_variant&non_coding_transcript_variant
33 splice_donor_region_variant&intron_variant
4 splice_donor_region_variant&intron_variant&nmd_transcript_variant
7 splice_donor_region_variant&intron_variant&non_coding_transcript_variant
19 splice_donor_variant
1 splice_donor_variant&nmd_transcript_variant
2 splice_donor_variant&non_coding_transcript_variant
3 splice_donor_variant&splice_donor_5th_base_variant&coding_sequence_variant&intron_variant
64 splice_polypyrimidine_tract_variant&intron_variant
6 splice_polypyrimidine_tract_variant&intron_variant&nmd_transcript_variant
8 splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant
2 splice_region_variant&3_prime_utr_variant
2 splice_region_variant&5_prime_utr_variant
4 splice_region_variant&intron_variant
6 splice_region_variant&non_coding_transcript_exon_variant
54 splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant
4 splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant&nmd_transcript_variant
5 splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant
27 splice_region_variant&synonymous_variant
13 start_lost
31 stop_gained
4 stop_gained&frameshift_variant
2 stop_gained&frameshift_variant&splice_region_variant
3 stop_gained&nmd_transcript_variant
2 stop_gained&splice_region_variant
2 stop_gained&splice_region_variant&nmd_transcript_variant
2 stop_lost
1 stop_lost&nmd_transcript_variant
6 stop_retained_variant
2 stop_retained_variant&nmd_transcript_variant
349 synonymous_variant
17 synonymous_variant&nmd_transcript_variant
1 transcript_ablation
2 upstream_gene_variant
** DONE [#B] Indicateurs qualité :qualité:
CLOSED: [2023-09-10 Sun 16:46]
*** Idée
Raredisease:
- FastQC : nombreuses statistiques. Non disponible Nix
- Mosdepth : calcule la profondeur (2x plus rapide que samtools depth). Nix
- MultiQC : fusionne juste les résultats des analyses. Non disponible nix
- Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics
- Qualimap : alternative fastqc ? Non disponible nix
- Sentieon's WgsMetricsAlgo : propriétaire
- TIDDIT's cov : TIDIT = remaninement chromosomique
Sarek:
- alignment statistics : samtools stats, mosdepth
- QC : MultiQC
MultiQC : non disponible Nix
*** DONE FastqQC
CLOSED: [2023-08-15 Tue 21:43] SCHEDULED: <2023-08-13 Sun>
*** DONE Mosdepth
CLOSED: [2023-08-15 Tue 21:43] SCHEDULED: <2023-08-13 Sun>
Pour exomple, il faut le fichier de capture
subworkflows/local/bam_markduplicates/
*** DONE Samtools stats
CLOSED: [2023-08-15 Tue 21:43] SCHEDULED: <2023-08-13 Sun>
*** DONE [#B] Compte-redu exécution avec MultiQC
CLOSED: [2023-08-15 Tue 21:43] SCHEDULED: <2023-08-13 Sun>
*** DONE Résultats sur NA12878 : 98% à 20x
CLOSED: [2023-08-19 Sat 20:45] SCHEDULED: <2023-08-17 Thu>
**** DONE Comprendre 91% à 20x seulement: SNVs inséré
CLOSED: [2023-08-18 Fri 22:25]
***** DONE Tester autre kit : Twist exome comprehensive
CLOSED: [2023-08-18 Fri 22:24]
Moins bon
***** DONE Tester génome sans alt
CLOSED: [2023-08-18 Fri 22:25]
Idem
***** DONE Tester NA12878 sans SNVs inséré: cause !!
CLOSED: [2023-08-18 Fri 22:25]
***** DONE Tester hg19 sur NA12878 non inséré
CLOSED: [2023-08-18 Fri 22:25]
**** DONE Comprendre pourquoi SNVs diminuent le score: reads manquants
CLOSED: [2023-08-19 Sat 20:34] SCHEDULED: <2023-08-18 Fri>
Voir [[id:5c1c36f3-f68e-4e6d-a7b6-61dca89abc37][Bug: perte de nombreux reads avec NA12878]]
*** DONE Relancer résultats avec NA1287 et NA12878 + sanger
CLOSED: [2023-08-29 Tue 10:30] SCHEDULED: <2023-08-29 Tue>
*** DONE Comparer avec hg19
CLOSED: [2023-08-28 Mon 17:22] SCHEDULED: <2023-08-20 Sun>
*** DONE Comparer avec autres kit de capture
CLOSED: [2023-08-28 Mon 17:22] SCHEDULED: <2023-08-20 Sun>
*** DONE Comparer avec no-alt
CLOSED: [2023-08-28 Mon 17:22] SCHEDULED: <2023-08-20 Sun>
** HOLD vérifier si normalisation
** KILL [#B] Vérification nomenclature hgvs :hgvs:
CLOSED: [2023-08-16 Wed 19:07] SCHEDULED: <2023-08-15 Tue>
*** KILL mutalyzer
CLOSED: [2023-08-16 Wed 19:07] SCHEDULED: <2023-08-13 Sun>
*** KILL API variantvalidator
CLOSED: [2023-08-16 Wed 19:07] SCHEDULED: <2023-08-13 Sun>
** DO