apraga/org - Change MCKPZLD66LQL3YIVEAQB4KPKXY3JL7ZAFGGWQVHCN4N65PGMQTDQC

Merge branch 'master' of git.sr.ht:~scut/org

Created by Alexis Praga on October 17, 2023

MCKPZLD66LQL3YIVEAQB4KPKXY3JL7ZAFGGWQVHCN4N65PGMQTDQC

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main

Change contents

Replacement in projects/bisonex.org at line 20 [6.35]

B:BD[5.4705] → [3.1206:9361]

_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
*** TODO Regarder annotation VEP des variants sur NA12878 non trataié :na12878:
SCHEDULED: <2023-10-16 Mon>
/Entered on/ [2023-10-16 Mon 19:39]
** 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

[7.12927]

[3.9361]

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
*** TODO Regarder annotation VEP des variants sur NA12878 non trataié :na12878:
SCHEDULED: <2023-10-16 Mon>
/Entered on/ [2023-10-16 Mon 19:39]
** 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

Deletion in projects/bisonex.org at line 79 [6.35]

B:BD[2.18417] → [2.18417:26399]

B:BD[7.12927] → [4.30:24563]

BD:BD[7.12927] → [4.30:24563]

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- [ ] 2300188800_63090616
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- [ ] 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
** TODO Variants manqués :missed:
SCHEDULED: <2023-10-21 Sat>
*** DONE 63012582: chr10:g.102230760 filtré par AD :63012582:
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
Il est en sortie d'haplotypecaller !
Attention à la position : POS=102230753  noté CG->C
GT:AD:DP:GQ:PL	0/1:26,8:34:99:146,0,671
Filtré par la condition AD <= 10 (porté par 8 reads seulement)
Non confirméen sanger, rendu vous
**** KILL image BAM cento
CLOSED: [2023-10-08 Sun 23:13]
**** DONE image BAM bisonex
CLOSED: [2023-10-08 Sun 23:23] SCHEDULED: <2023-10-08 Sun>
**** DONE Mail Paul
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
*** DONE 63060439: chr15:g.26869324 = Problème de profondeur DP=15 :63060439:
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
GABRA5
Rendu VOUS avec un variant patho MDB5 pour même patient (VOUS- même)
Non confirmé en Sanger
GT:AD:DP:GQ:PL 0/1:9,6:15:99:103,0,213
**** DONE image BAM bisonex
CLOSED: [2023-10-08 Sun 22:56]
**** DONE Mail Paul
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
*** TODO Ajouter négatifs dans la liste des variants
SCHEDULED: <2023-10-19 Thu>
* Résultats
** TODO Speed-up BWA-mem
SCHEDULED: <2023-10-22 Sun>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-10-22 Sun>
* Communication
** DONE Mail NGS-diag
CLOSED: [2023-10-06 Fri 08:04] SCHEDULED: <2023-10-06 Fri>
/Entered on/ [2023-10-04 Wed 19:33]
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

Solving an order conflict in projects/bisonex.org at line 79 [6.35]
[2.18417]

Insertion in projects/bisonex.org at line 79 [6.35]

[0.24528]

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- [ ] 2300188800_63090616
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- [ ] 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
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** TODO Variants manqués :missed:
SCHEDULED: <2023-10-21 Sat>
*** DONE 63012582: chr10:g.102230760 filtré par AD :63012582:
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
Il est en sortie d'haplotypecaller !
Attention à la position : POS=102230753  noté CG->C
GT:AD:DP:GQ:PL	0/1:26,8:34:99:146,0,671
Filtré par la condition AD <= 10 (porté par 8 reads seulement)
Non confirméen sanger, rendu vous
**** KILL image BAM cento
CLOSED: [2023-10-08 Sun 23:13]
**** DONE image BAM bisonex
CLOSED: [2023-10-08 Sun 23:23] SCHEDULED: <2023-10-08 Sun>
**** DONE Mail Paul
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
*** DONE 63060439: chr15:g.26869324 = Problème de profondeur DP=15 :63060439:
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
GABRA5
Rendu VOUS avec un variant patho MDB5 pour même patient (VOUS- même)
Non confirmé en Sanger
GT:AD:DP:GQ:PL 0/1:9,6:15:99:103,0,213
**** DONE image BAM bisonex
CLOSED: [2023-10-08 Sun 22:56]
**** DONE Mail Paul
CLOSED: [2023-10-08 Sun 23:24] SCHEDULED: <2023-10-08 Sun>
*** TODO Ajouter négatifs dans la liste des variants
SCHEDULED: <2023-10-19 Thu>
* Résultats
** TODO Speed-up BWA-mem
SCHEDULED: <2023-10-22 Sun>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-10-22 Sun>
* Communication
** DONE Mail NGS-diag
CLOSED: [2023-10-06 Fri 08:04] SCHEDULED: <2023-10-06 Fri>
/Entered on/ [2023-10-04 Wed 19:33]