apraga/org - Change DTRJKVJ24X2JZEXXX6W53VJQQNU2OMXE5R5ML3VOI2XQSWYCJXYAC

Updating cento list

Created by Alexis Praga on October 22, 2023

DTRJKVJ24X2JZEXXX6W53VJQQNU2OMXE5R5ML3VOI2XQSWYCJXYAC

Dependencies

In channels

main

Change contents

Insertion in workout.org at line 6776 [3.1]

[2.82]

* <2023-10-22 Sun> Workout
** RTO
- 33-24
** L-sit
-
** Muscle-up
- 1
- 2-1-1
- 2-1-1
- 1-1-1
** Pistols :
- 3
- 3
- 3
** Norwegian roll
- 3
- 3
- 3

Replacement in projects/bisonex.org at line 2 [5.35]

B:BD[4.5112] → [2.442:8634]

ub.com/NixOS/nixpkgs/issues/192396][Bug report Version 22.10.6]]
**** Notes
Erreur :
ERROR: Cannot download nextflow required file -- make sure you can connect to the internet
Alternatively you can try to download this file:
    https://www.nextflow.io/releases/v22.10.6/nextflow-22.10.6-all.jar
and save it as:
    .//nix/store/md2b1ah4d7ivj82k8xxap30dmdci00pa-nextflow-22.10.6/bin/.nextflow-wrapped
Dans la mise à jour, il y a la création d'un environnement virtuel qui casse l'exécution de nextflow (besoin de télécharger)
Fix = désactiver
**** KILL Patch NXF_OFFLINE=true
CLOSED: [2023-07-02 Sun 11:02] SCHEDULED: <2023-06-11 Sun>
** WAIT [[https://github.com/NixOS/nixpkgs/pull/249329][Multiqc]]
HG002,sanger-chr20,data/HG002-sanger-inserted-chr20_1.fq.gz,data/HG002-sanger-inserted-chr20_2.fq.gz
** KILL Mutalyzer
CLOSED: [2023-08-16 Wed 19:07] SCHEDULED: <2023-08-13 Sun>
Packaging faisable mais nombreux paquet python
** TODO Variant validator -> hgvs
C'est juste une interface autour d'hgvs mais il faut
- postgresql
- un accès ou télécharger des bases de données
  Dépendences
  s: wcwidth, pyee, pure-eval, ptyprocess, pickleshare, parsley, parse, fake-useragent, executing, backcall, appdirs, zipp, websockets, w3lib, urllib3, traitlets, tqdm, tabulate, sqlparse, soupsieve, six, pygments, psycopg2, prompt-toolkit, pexpect, parso, lxml, idna, humanfriendly, decorator, cython, cssselect, configparser, charset-normalizer, certifi, attrs, requests, pysam, pyquery, matplotlib-inline, jedi, importlib-metadata, coloredlogs, beautifulsoup4, asttokens, yoyo-migrations, stack-data, pyppeteer, bs4, bioutils, requests-html, ipython, biocommons.seqrepo, hgvs
** TODO SPIP T2T
*** DONE PR upstream
CLOSED: [2023-08-12 Sat 18:23] SCHEDULED: <2023-08-12 Sat 18:00>
*** DONE Mail R. Lemann
CLOSED: [2023-08-12 Sat 18:23] SCHEDULED: <2023-08-12 Sat 18:00>
*** TODO Mise à jour packages nix
** TODO VEP :vep:
*** DONE [[https://github.com/NixOS/nixpkgs/pull/185691][BioPerl]]
SCHEDULED: <2022-08-10 Wed>
/Entered on/ [2022-08-09 Tue 10:57]
PR submitted
*** TODO BioDBBBigFile
:PROPERTIES:
:ORDERED:  t
:END:
/Entered on/ [2022-08-10 Wed 14:28]
On utilise la dernière version de kent, donc plus de problème.
PRête à être mergé. Rebase faite<2023-07-02 Sun>
**** DONE Version de kent déjà packagée : forcer version  335
CLOSED: [2023-07-02 Sun 11:20]
***** KILL [[https://github.com/NixOS/nixpkgs/pull/206991][Restore building kent 404]]
CLOSED: [2023-05-06 Sat 17:40]
Review faite <2023-03-26 Sun> , atteinte merge]
Relancé <2023-05-06 Sat>
Kent 446 n'a pas ce problème donc PR inutile
***** DONE [[https://github.com/NixOS/nixpkgs/pull/223411][Ajouter les header to package]] (inc folder)
CLOSED: [2023-05-08 Mon 10:18] SCHEDULED: <2023-05-07 Sun>
Review à faire
https://github.com/NixOS/nixpkgs/pull/223411
Corrigé et plus besoin de la PR précédente
***** KILL [[https://github.com/NixOS/nixpkgs/pull/186462][BioDBBBigFile]] avec ces 2 changements
CLOSED: [2023-07-02 Sun 11:20]
**** KILL Version de kent déjà packagée : 404
CLOSED: [2023-03-27 Mon 16:43]
Compile mais les tests de passent pas
**** DONE Modifier selon PR https://github.com/NixOS/nixpkgs/pull/186462
CLOSED: [2023-07-30 Sun 22:01] SCHEDULED: <2023-07-30 Sun 20:00>
:LOGBOOK:
CLOCK: [2023-07-30 Sun 19:13]--[2023-07-30 Sun 20:50] =>  1:37
:END:
Modification nécessaire pour kent :
- plus de patch
- suppression d'une boucle dans postPatch
On supprime aussi NIX_BUILD_TOP
**** TODO Corriger PR biobigfile
SCHEDULED: <2023-10-21 Sat>
/Entered on/ [2023-10-15 Sun 17:21]
*** DONE [[https://github.com/NixOS/nixpkgs/pull/186459][BioDBHTS]]
CLOSED: [2023-05-06 Sat 08:49] SCHEDULED: <2023-04-15 Sat>
/Entered on/ [2022-08-10 Wed 14:28]
Correction pour review faites <2022-10-10 Mon>
*** DONE [[https://github.com/NixOS/nixpkgs/pull/186464][BioExtAlign]]
CLOSED: [2022-10-22 Sat 12:43] SCHEDULED: <2022-08-10 Wed>
/Entered on/ [2022-08-10 Wed 14:28]
Review <2022-10-10 Mon>, correction dans la journée.
Correction 2e passe, attente
Impossible de faire marcher les tests Car il ne trouve pas le module Bio::Tools::Align, qui est dans un dossier ailleurs dans le dépôt. Même en compilant tout le dépôt, cela ne fonctionne pas... On skip les tests.
*** TODO VEP
** WAIT [[https://github.com/NixOS/nixpkgs/pull/230394][rtg-tools]] :vcfeval:
Soumis
** WAIT Package Spip https://github.com/NixOS/nixpkgs/pull/247476
** TODO Happy :happy:
*** TODO PR python 3 upstream
SCHEDULED: <2023-10-22 Sun>
*** TODO nixpkgs en l'état
SCHEDULED: <2023-10-22 Sun>
** PROJ SpliceAI
** TODO Bamsurgeon
/Entered on/ [2023-05-13 Sat 19:11]
*** TODO Velvet
** TODO PR Picard avec option pour gérer la mémoire
Similaire à
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/picard/picard.sh
* Julia :julia:
** KILL XAM.jl: PR pour modification record :julia:
CLOSED: [2023-05-29 Mon 15:40] SCHEDULED: <2023-05-28 Sun>
/Entered on/ [2023-05-27 Sat 22:39]
** TODO XAMscissors.jl :xamscissors:
Modification de la séquence dans BAM.
*Pas de mise à jour de CIGAR*
On convertit en fastq et on lance le pipeline pour "corriger"
#+begin_src sh
cd /home/alex/code/bisonex/out/63003856/preprocessing/mapped
samtools view 63003856_S135.bam NC_000022.11 -o 63003856_S135_chr22.bam
cd /home/alex/recherche/bisonex/code/BamScissors.jl
cp ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135_chr22.bam .
samtools index 63003856_chr22.bam
#+end_src
Le script va modifier le bam, le trier et générer le fastq. !!!
Attention: ne pas oublier l'option -n !!!
#+begin_src sh
time julia --project=.. insertVariant.jl
scp 63003856_S135_chr22_{1,2}.fq.gz meso:/Work/Users/apraga/bisonex/tests/bamscissors/
#+end_src
*** WAIT Implémenter les SNV avec VAF :snv:
Stratégie :
1. calculer la profondeur sur les positions
2. créer un dictionnaire { nom du reads : position dataframe }
3. itérer sur tous les reads et changer ceux marqués
**** DONE VAF = 1
CLOSED: [2023-05-29 Mon 15:34]
**** DONE VAF selon loi normale
CLOSED: [2023-05-29 Mon 15:35]
Tronquée si > 1
**** WAIT Tests unitaires
***** DONE NA12878: 1 gène sur chromosome 22
CLOSED: [2023-05-30 Tue 23:55]
root = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/"
#+begin_src sh
samtools view project.NIST_NIST7035_H7AP8ADXX_NA12878.bwa.markDuplicates.bam  chr22 -o project.NIST_NIST7035_H7AP8ADXX_NA12878_chr22.bam
samtools view project.NIST_NIST7035_H7AP8ADXX_NA12878_chr22.bam chr22:19419700-19424000 -o NIST7035_H7AP8ADXX_NA12878_chr22_MRPL40_hg19.bam
#+end_src
***** WAIT Pull request formatspeciment
https://github.com/BioJulia/FormatSpecimens.jl/pull/8
***** DONE Formatspecimens
CLOSED: [2023-05-29 Mon 23:03]
****** DONE 1 read
CLOSED: [2023-05-29 Mon 23:02]
****** DONE VAF sur 1 exon
CLOSED: [2023-05-29 Mon 23:03]
**** DONE [#A] Bug: perte de nombreux reads avec NA12878
CLOSED: [2023-08-19 Sat 20:45] SCHEDULED: <2023-08-18 Fri>
:PROPERTIES:
:ID:       5c1c36f3-f68e-4e6d-a7b6-61dca89abc37
:END:
Ex: chrX:g.124056226 : on passe de 65 reads à 1
Test xamscissors: pas de soucis...
On teste sur cette position +/- 200bp
#+begin_src sh :dir /home/alex/roam/research/bisonex/code/sanger
samtools view   /home/alex/code/bisonex/out/2300346867_NA12878-63118093_S260-GRCh38/preprocessing/mapped/2300346867_NA12878-63118093_S260-GRCh38.bam chrX:124056026-124056426 -o chrXsmall.bam
#+end_src
#+RESULTS:
***** DONE Vérifier profondeur avec dernière version :
CLOSED: [2023-08-19 Sat 20:34] SCHEDULED: <2023-08-19 Sat>
****** DONE chr20: profondeur ok
SCHEDULED: <2023-08-19 Sat>
****** DONE toutes les données
CLOSED: [2023-08-19 Sat 20:34] SCHEDULED: <2023-08-19 Sat>
Ok pour 7 variants (IGV) notament chromosome X
*** TODO Implémenter les indel avec VAF :indel:
*** TODO Soumission paquet
* Données
:PROPERTIES:
:CATEGORY: data
:END:
** DONE Remplacer bam par fastq sur mesocentre
CLOSED: [2023-04-16 Sun 16:33]
Commande
*** DONE Supprimer les fastq non "paired"
CLOSED: [2023

[4.5112]

[6.10603]

ub.com/NixOS/nixpkgs/issues/192396][Bug report Version 22.10.6]]
**** Notes
Erreur :
ERROR: Cannot download nextflow required file -- make sure you can connect to the internet
Alternatively you can try to download this file:
    https://www.nextflow.io/releases/v22.10.6/nextflow-22.10.6-all.jar
and save it as:
    .//nix/store/md2b1ah4d7ivj82k8xxap30dmdci00pa-nextflow-22.10.6/bin/.nextflow-wrapped
Dans la mise à jour, il y a la création d'un environnement virtuel qui casse l'exécution de nextflow (besoin de télécharger)
Fix = désactiver
**** KILL Patch NXF_OFFLINE=true
CLOSED: [2023-07-02 Sun 11:02] SCHEDULED: <2023-06-11 Sun>
** WAIT [[https://github.com/NixOS/nixpkgs/pull/249329][Multiqc]]
HG002,sanger-chr20,data/HG002-sanger-inserted-chr20_1.fq.gz,data/HG002-sanger-inserted-chr20_2.fq.gz
** KILL Mutalyzer
CLOSED: [2023-08-16 Wed 19:07] SCHEDULED: <2023-08-13 Sun>
Packaging faisable mais nombreux paquet python
** TODO Variant validator -> hgvs
C'est juste une interface autour d'hgvs mais il faut
- postgresql
- un accès ou télécharger des bases de données
  Dépendences
  s: wcwidth, pyee, pure-eval, ptyprocess, pickleshare, parsley, parse, fake-useragent, executing, backcall, appdirs, zipp, websockets, w3lib, urllib3, traitlets, tqdm, tabulate, sqlparse, soupsieve, six, pygments, psycopg2, prompt-toolkit, pexpect, parso, lxml, idna, humanfriendly, decorator, cython, cssselect, configparser, charset-normalizer, certifi, attrs, requests, pysam, pyquery, matplotlib-inline, jedi, importlib-metadata, coloredlogs, beautifulsoup4, asttokens, yoyo-migrations, stack-data, pyppeteer, bs4, bioutils, requests-html, ipython, biocommons.seqrepo, hgvs
** TODO SPIP T2T
*** DONE PR upstream
CLOSED: [2023-08-12 Sat 18:23] SCHEDULED: <2023-08-12 Sat 18:00>
*** DONE Mail R. Lemann
CLOSED: [2023-08-12 Sat 18:23] SCHEDULED: <2023-08-12 Sat 18:00>
*** TODO Mise à jour packages nix
** TODO VEP :vep:
*** DONE [[https://github.com/NixOS/nixpkgs/pull/185691][BioPerl]]
SCHEDULED: <2022-08-10 Wed>
/Entered on/ [2022-08-09 Tue 10:57]
PR submitted
*** TODO BioDBBBigFile
:PROPERTIES:
:ORDERED:  t
:END:
/Entered on/ [2022-08-10 Wed 14:28]
On utilise la dernière version de kent, donc plus de problème.
PRête à être mergé. Rebase faite<2023-07-02 Sun>
**** DONE Version de kent déjà packagée : forcer version  335
CLOSED: [2023-07-02 Sun 11:20]
***** KILL [[https://github.com/NixOS/nixpkgs/pull/206991][Restore building kent 404]]
CLOSED: [2023-05-06 Sat 17:40]
Review faite <2023-03-26 Sun> , atteinte merge]
Relancé <2023-05-06 Sat>
Kent 446 n'a pas ce problème donc PR inutile
***** DONE [[https://github.com/NixOS/nixpkgs/pull/223411][Ajouter les header to package]] (inc folder)
CLOSED: [2023-05-08 Mon 10:18] SCHEDULED: <2023-05-07 Sun>
Review à faire
https://github.com/NixOS/nixpkgs/pull/223411
Corrigé et plus besoin de la PR précédente
***** KILL [[https://github.com/NixOS/nixpkgs/pull/186462][BioDBBBigFile]] avec ces 2 changements
CLOSED: [2023-07-02 Sun 11:20]
**** KILL Version de kent déjà packagée : 404
CLOSED: [2023-03-27 Mon 16:43]
Compile mais les tests de passent pas
**** DONE Modifier selon PR https://github.com/NixOS/nixpkgs/pull/186462
CLOSED: [2023-07-30 Sun 22:01] SCHEDULED: <2023-07-30 Sun 20:00>
:LOGBOOK:
CLOCK: [2023-07-30 Sun 19:13]--[2023-07-30 Sun 20:50] =>  1:37
:END:
Modification nécessaire pour kent :
- plus de patch
- suppression d'une boucle dans postPatch
On supprime aussi NIX_BUILD_TOP
**** TODO Corriger PR biobigfile
SCHEDULED: <2023-10-21 Sat>
/Entered on/ [2023-10-15 Sun 17:21]
*** DONE [[https://github.com/NixOS/nixpkgs/pull/186459][BioDBHTS]]
CLOSED: [2023-05-06 Sat 08:49] SCHEDULED: <2023-04-15 Sat>
/Entered on/ [2022-08-10 Wed 14:28]
Correction pour review faites <2022-10-10 Mon>
*** DONE [[https://github.com/NixOS/nixpkgs/pull/186464][BioExtAlign]]
CLOSED: [2022-10-22 Sat 12:43] SCHEDULED: <2022-08-10 Wed>
/Entered on/ [2022-08-10 Wed 14:28]
Review <2022-10-10 Mon>, correction dans la journée.
Correction 2e passe, attente
Impossible de faire marcher les tests Car il ne trouve pas le module Bio::Tools::Align, qui est dans un dossier ailleurs dans le dépôt. Même en compilant tout le dépôt, cela ne fonctionne pas... On skip les tests.
*** TODO VEP
** WAIT [[https://github.com/NixOS/nixpkgs/pull/230394][rtg-tools]] :vcfeval:
Soumis
** WAIT Package Spip https://github.com/NixOS/nixpkgs/pull/247476
** TODO Happy :happy:
*** TODO PR python 3 upstream
SCHEDULED: <2023-10-29 Sun>
*** TODO nixpkgs en l'état
SCHEDULED: <2023-10-29 Sun>
** PROJ SpliceAI
** TODO Bamsurgeon
/Entered on/ [2023-05-13 Sat 19:11]
*** TODO Velvet
** TODO PR Picard avec option pour gérer la mémoire
Similaire à
https://github.com/bioconda/bioconda-recipes/blob/master/recipes/picard/picard.sh
* Julia :julia:
** KILL XAM.jl: PR pour modification record :julia:
CLOSED: [2023-05-29 Mon 15:40] SCHEDULED: <2023-05-28 Sun>
/Entered on/ [2023-05-27 Sat 22:39]
** TODO XAMscissors.jl :xamscissors:
Modification de la séquence dans BAM.
*Pas de mise à jour de CIGAR*
On convertit en fastq et on lance le pipeline pour "corriger"
#+begin_src sh
cd /home/alex/code/bisonex/out/63003856/preprocessing/mapped
samtools view 63003856_S135.bam NC_000022.11 -o 63003856_S135_chr22.bam
cd /home/alex/recherche/bisonex/code/BamScissors.jl
cp ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135_chr22.bam .
samtools index 63003856_chr22.bam
#+end_src
Le script va modifier le bam, le trier et générer le fastq. !!!
Attention: ne pas oublier l'option -n !!!
#+begin_src sh
time julia --project=.. insertVariant.jl
scp 63003856_S135_chr22_{1,2}.fq.gz meso:/Work/Users/apraga/bisonex/tests/bamscissors/
#+end_src
*** WAIT Implémenter les SNV avec VAF :snv:
Stratégie :
1. calculer la profondeur sur les positions
2. créer un dictionnaire { nom du reads : position dataframe }
3. itérer sur tous les reads et changer ceux marqués
**** DONE VAF = 1
CLOSED: [2023-05-29 Mon 15:34]
**** DONE VAF selon loi normale
CLOSED: [2023-05-29 Mon 15:35]
Tronquée si > 1
**** WAIT Tests unitaires
***** DONE NA12878: 1 gène sur chromosome 22
CLOSED: [2023-05-30 Tue 23:55]
root = "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/"
#+begin_src sh
samtools view project.NIST_NIST7035_H7AP8ADXX_NA12878.bwa.markDuplicates.bam  chr22 -o project.NIST_NIST7035_H7AP8ADXX_NA12878_chr22.bam
samtools view project.NIST_NIST7035_H7AP8ADXX_NA12878_chr22.bam chr22:19419700-19424000 -o NIST7035_H7AP8ADXX_NA12878_chr22_MRPL40_hg19.bam
#+end_src
***** WAIT Pull request formatspeciment
https://github.com/BioJulia/FormatSpecimens.jl/pull/8
***** DONE Formatspecimens
CLOSED: [2023-05-29 Mon 23:03]
****** DONE 1 read
CLOSED: [2023-05-29 Mon 23:02]
****** DONE VAF sur 1 exon
CLOSED: [2023-05-29 Mon 23:03]
**** DONE [#A] Bug: perte de nombreux reads avec NA12878
CLOSED: [2023-08-19 Sat 20:45] SCHEDULED: <2023-08-18 Fri>
:PROPERTIES:
:ID:       5c1c36f3-f68e-4e6d-a7b6-61dca89abc37
:END:
Ex: chrX:g.124056226 : on passe de 65 reads à 1
Test xamscissors: pas de soucis...
On teste sur cette position +/- 200bp
#+begin_src sh :dir /home/alex/roam/research/bisonex/code/sanger
samtools view   /home/alex/code/bisonex/out/2300346867_NA12878-63118093_S260-GRCh38/preprocessing/mapped/2300346867_NA12878-63118093_S260-GRCh38.bam chrX:124056026-124056426 -o chrXsmall.bam
#+end_src
#+RESULTS:
***** DONE Vérifier profondeur avec dernière version :
CLOSED: [2023-08-19 Sat 20:34] SCHEDULED: <2023-08-19 Sat>
****** DONE chr20: profondeur ok
SCHEDULED: <2023-08-19 Sat>
****** DONE toutes les données
CLOSED: [2023-08-19 Sat 20:34] SCHEDULED: <2023-08-19 Sat>
Ok pour 7 variants (IGV) notament chromosome X
*** TODO Implémenter les indel avec VAF :indel:
*** TODO Soumission paquet
* Données
:PROPERTIES:
:CATEGORY: data
:END:
** DONE Remplacer bam par fastq sur mesocentre
CLOSED: [2023-04-16 Sun 16:33]
Commande
*** DONE Supprimer les fastq non "paired"
CLOSED: [2023

Replacement in projects/bisonex.org at line 64 [5.35]

B:BD[7.31954] → [2.8635:16827]

 donnés dans publication https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8354858/
#+begin_quote
In short, the Nextera Rapid Capture Exome Kit (Illumina, San Diego, CA), the SureSelect Human All Exon kit (Agilent, Santa Clara, CA) or the Twist Human Core Exome was used for enrichment, and a Nextseq500, HiSeq4000, or Novoseq 6000 (Illumina) instrument was used for the actual sequencing, with the average coverage targeted to at least 100× or at least 98% of the target DNA covered 20×.
#+end_quote
Par défaut, on utilisera https://www.twistbioscience.com/products/ngs/alliance-panels#tab-3
ANnonce récente pour nouveau panel Twist : https://www.centogene.com/news-events/news/newsdetails/twist-bioscience-and-centogene-launch-three-panels-to-advance-rare-disease-and-hereditary-cancer-research-and-support-diagnostics
Masi pas de fichier BED
***** DONE Mail centogène
CLOSED: [2023-07-30 Sun 14:22] DEADLINE: <2023-07-23 Sun>
**** DONE Tester Nextera Rapid Capture Exome v1.2 (hg19) :giab:
CLOSED: [2023-08-06 Sun 19:05] SCHEDULED: <2023-08-03 Thu 19:00>
https://support.illumina.com/downloads/nextera-rapid-capture-exome-v1-2-product-files.html
***** DONE Liftover capture
CLOSED: [2023-08-06 Sun 18:30] SCHEDULED: <2023-08-06 Sun>
#+begin_src sh
 nextflow run -profile standard,helios workflows/lift-nextera-capture.nf  -lib lib
#+end_src
Vérification rapide : ok
***** DONE Run
CLOSED: [2023-08-06 Sun 19:05] SCHEDULED: <2023-08-06 Sun>
#+begin_src sh
 nextflow run workflows/compareVCF.nf -profile standard,helios --query=out/2300346867_NA12878-63118093_S260-GRCh38/callVariant/haplotypecaller/2300346867_NA12878-63118093_S260-GRCh38.vcf.gz --outdir=out/2300346867_NA12878-63118093_S260-GRCh38/happy-nextera-lifted/ --compare=happy -lib lib --capture=capture/nexterarapidcapture_exome_targetedregions_v1.2-nochrM_lifted.bed  --id=HG001 --genome=GRCh38
#+end_src
**** DONE Tester Agilent SureSelect All Exon V8 (hg38) :giab:
CLOSED: [2023-07-31 Mon 23:09] SCHEDULED: <2023-07-31 Mon>
https://earray.chem.agilent.com/suredesign/index.htm
"Find design"
"Agilent catalog"
Fichiers:
- Regions.bed: Targeted exon intervals, curated and targeted by Agilent Technologies
- MergedProbes.bed: Merged probes for targeted enrichment of exons described in Regions.bed
- Covered.bed: Merged probes and sequences with 95% homology or above
- Padded.bed: Merged probes and sequences with 95% homology or above extended 50 bp at each side
- AllTracks.bed: Targeted regions and covered tracks
 #+begin_src sh
nextflow run workflows/compareVCF.nf -profile standard,helios --query=out/2300346867_63118093_NA12878-GRCh38/callVariant/haplotypecaller/2300346867_63118093_NA12878-GRCh38.vcf.gz --outdir=out/2300346867_63118093_NA12878-GRCh38/happy/ --compare=happy -lib lib --capture=capture/Agilent_SureSelect_All_Exons_v8_hg38_Regions.bed  --id=HG001 --genome=GRCh38
 #+end_src
| Type  | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
| INDEL | ALL    |         423 |      395 |       28 |         915 |      108 |       405 |     4 |    13 |      0.933806 |         0.788235 |       0.442623 |        0.854868 |                        |                        |        1.7012987012987013 |        2.7916666666666665 |
| INDEL | PASS   |         423 |      395 |       28 |         915 |      108 |       405 |     4 |    13 |      0.933806 |         0.788235 |       0.442623 |        0.854868 |                        |                        |        1.7012987012987013 |        2.7916666666666665 |
| SNP   | ALL    |       20984 |    20600 |      384 |       26080 |      780 |      4703 |    62 |    10 |        0.9817 |         0.963512 |        0.18033 |        0.972521 |     3.0499710592321048 |     2.7596541786743516 |          1.58256372367935 |        1.8978207694018234 |
| SNP   | PASS   |       20984 |    20600 |      384 |       26080 |      780 |      4703 |    62 |    10 |        0.9817 |         0.963512 |        0.18033 |        0.972521 |     3.0499710592321048 |     2.7596541786743516 |          1.58256372367935 |        1.8978207694018234 |
**** DONE Test Twist Human core Exome (hg38):giab:
CLOSED: [2023-08-01 Tue 23:16] SCHEDULED: <202 3-08-02 Wed>
https://www.twistbioscience.com/resources/data-files/ngs-human-core-exome-panel-bed-file
#+begin_src
nextflow run workflows/compareVCF.nf -profile standard,helios --query=out/2300346867_63118093_NA12878-GRCh38/callVariant/haplotypecaller/2300346867_63118093_NA12878-GRCh38.vcf.gz --outdir=out/2300346867_63118093_NA12878-GRCh38/happy-twist-exome-core/ --compare=happy -lib lib --capture=capture/Twist_Exome_Core_Covered_Targets_hg38.bed  --id=HG001 --genome=GRCh38 -bg
#+end_src
| Type  | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
| INDEL | ALL    |         328 |      313 |       15 |         722 |       95 |       309 |     4 |    13 |      0.954268 |         0.769976 |       0.427978 |        0.852273 |                        |                        |        1.8584070796460177 |        2.8967391304347827 |
| INDEL | PASS   |         328 |      313 |       15 |         722 |       95 |       309 |     4 |    13 |      0.954268 |         0.769976 |       0.427978 |        0.852273 |                        |                        |        1.8584070796460177 |        2.8967391304347827 |
| SNP   | ALL    |       19198 |    18962 |      236 |       23381 |      684 |      3738 |    48 |    10 |      0.987707 |         0.965178 |       0.159873 |        0.976313 |     3.1034188034188035 |      2.859264147830391 |        1.5669565217391304 |        1.8578767123287672 |
| SNP   | PASS   |       19198 |    18962 |      236 |       23381 |      684 |      3738 |    48 |    10 |      0.987707 |         0.965178 |       0.159873 |        0.976313 |     3.1034188034188035 |      2.859264147830391 |        1.5669565217391304 |        1.8578767123287672 |
**** DONE Test Twist Human core Exome (hg38):giab:
CLOSED: [2023-08-05 Sat 09:25] SCHEDULED: <2023-08-03 Thu 20:00>
#+begin_src sh
ID="2300346867_NA12878-63118093_S260-GRCh38"; nextflow run workflows/compareVCF.nf -profile standard,helios --query=out/${ID}/callVariant/haplotypecaller/${ID}.vcf.gz --outdir=out/${ID}/happy-twist-exome-core/ --compare=happy -lib lib --capture=capture/Twist_Exome_Core_Covered_Targets_hg38.bed  --id=HG001 --genome=GRCh38 -bg
#+end_src
**** DONE Tester Agilen SureSelect All Exon V8 (hg38) GATK-4.4:giab:
CLOSED: [2023-08-05 Sat 09:25] SCHEDULED: <2023-08-03 Thu 20:00>
**** DONE Vérifier l'impact gatk 4.3 - 4.4 : aucun
CLOSED: [2023-08-05 Sat 09:25]
**** DONE Figure comparant les 3 capture :hg001:
CLOSED: [2023-08-06 Sun 20:24] SCHEDULED: <2023-08-06 Sun>
**** DONE Mail Paul sur  les 3 capture :hg001:
CLOSED: [2023-08-06 Sun 20:24] SCHEDULED: <2023-08-06 Sun>
**** KILL Tester si le panel Twist Alliance VCGS Exome suffit
CLOSED: [2023-07-31 Mon 22:31] SCHEDULED: <2023-07-30 Sun>
**** DONE Mail cento pour demande le type de capture
CLOSED: [2023-10-07 Sat 17:59]
/Entered on/ [2023-08-07 Mon 20:40]
Twist exome
*** PROJ Comparer happy et happy-vcfeval :giab:
** TODO Données CHM13 :chm:
https://github.com/lh3/CHM-eval
*** TODO Run ERR1341793
SCHEDULED: <2023-10-22 Sun>
(raw reads ERR1341793_1.fastq.gz and ERR1341793_2.fastq.gz downloaded from https://www.ebi.ac.uk/ena/browser/view/ERR1341793)
*** TODO Run ERR1341796
SCHEDULED: <2023-10-22 Sun>
** TODO Insilico :cento:
*** TODO tous les variants centogène
**** DONE Extraire liste des SNVs
CLOSED: [2023-04-22 Sat 17:32] SCHEDULED: <2023-04-17 Mon>
***** DONE Corriger manquant à la main
CLOSED: [2023-04-22 Sat 17:31]
La sortie est sauvegardé dans git-annex : variants_success.csv
***** DONE Automa

[7.31954]

[8.14472]

 donnés dans publication https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8354858/
#+begin_quote
In short, the Nextera Rapid Capture Exome Kit (Illumina, San Diego, CA), the SureSelect Human All Exon kit (Agilent, Santa Clara, CA) or the Twist Human Core Exome was used for enrichment, and a Nextseq500, HiSeq4000, or Novoseq 6000 (Illumina) instrument was used for the actual sequencing, with the average coverage targeted to at least 100× or at least 98% of the target DNA covered 20×.
#+end_quote
Par défaut, on utilisera https://www.twistbioscience.com/products/ngs/alliance-panels#tab-3
ANnonce récente pour nouveau panel Twist : https://www.centogene.com/news-events/news/newsdetails/twist-bioscience-and-centogene-launch-three-panels-to-advance-rare-disease-and-hereditary-cancer-research-and-support-diagnostics
Masi pas de fichier BED
***** DONE Mail centogène
CLOSED: [2023-07-30 Sun 14:22] DEADLINE: <2023-07-23 Sun>
**** DONE Tester Nextera Rapid Capture Exome v1.2 (hg19) :giab:
CLOSED: [2023-08-06 Sun 19:05] SCHEDULED: <2023-08-03 Thu 19:00>
https://support.illumina.com/downloads/nextera-rapid-capture-exome-v1-2-product-files.html
***** DONE Liftover capture
CLOSED: [2023-08-06 Sun 18:30] SCHEDULED: <2023-08-06 Sun>
#+begin_src sh
 nextflow run -profile standard,helios workflows/lift-nextera-capture.nf  -lib lib
#+end_src
Vérification rapide : ok
***** DONE Run
CLOSED: [2023-08-06 Sun 19:05] SCHEDULED: <2023-08-06 Sun>
#+begin_src sh
 nextflow run workflows/compareVCF.nf -profile standard,helios --query=out/2300346867_NA12878-63118093_S260-GRCh38/callVariant/haplotypecaller/2300346867_NA12878-63118093_S260-GRCh38.vcf.gz --outdir=out/2300346867_NA12878-63118093_S260-GRCh38/happy-nextera-lifted/ --compare=happy -lib lib --capture=capture/nexterarapidcapture_exome_targetedregions_v1.2-nochrM_lifted.bed  --id=HG001 --genome=GRCh38
#+end_src
**** DONE Tester Agilent SureSelect All Exon V8 (hg38) :giab:
CLOSED: [2023-07-31 Mon 23:09] SCHEDULED: <2023-07-31 Mon>
https://earray.chem.agilent.com/suredesign/index.htm
"Find design"
"Agilent catalog"
Fichiers:
- Regions.bed: Targeted exon intervals, curated and targeted by Agilent Technologies
- MergedProbes.bed: Merged probes for targeted enrichment of exons described in Regions.bed
- Covered.bed: Merged probes and sequences with 95% homology or above
- Padded.bed: Merged probes and sequences with 95% homology or above extended 50 bp at each side
- AllTracks.bed: Targeted regions and covered tracks
 #+begin_src sh
nextflow run workflows/compareVCF.nf -profile standard,helios --query=out/2300346867_63118093_NA12878-GRCh38/callVariant/haplotypecaller/2300346867_63118093_NA12878-GRCh38.vcf.gz --outdir=out/2300346867_63118093_NA12878-GRCh38/happy/ --compare=happy -lib lib --capture=capture/Agilent_SureSelect_All_Exons_v8_hg38_Regions.bed  --id=HG001 --genome=GRCh38
 #+end_src
| Type  | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
| INDEL | ALL    |         423 |      395 |       28 |         915 |      108 |       405 |     4 |    13 |      0.933806 |         0.788235 |       0.442623 |        0.854868 |                        |                        |        1.7012987012987013 |        2.7916666666666665 |
| INDEL | PASS   |         423 |      395 |       28 |         915 |      108 |       405 |     4 |    13 |      0.933806 |         0.788235 |       0.442623 |        0.854868 |                        |                        |        1.7012987012987013 |        2.7916666666666665 |
| SNP   | ALL    |       20984 |    20600 |      384 |       26080 |      780 |      4703 |    62 |    10 |        0.9817 |         0.963512 |        0.18033 |        0.972521 |     3.0499710592321048 |     2.7596541786743516 |          1.58256372367935 |        1.8978207694018234 |
| SNP   | PASS   |       20984 |    20600 |      384 |       26080 |      780 |      4703 |    62 |    10 |        0.9817 |         0.963512 |        0.18033 |        0.972521 |     3.0499710592321048 |     2.7596541786743516 |          1.58256372367935 |        1.8978207694018234 |
**** DONE Test Twist Human core Exome (hg38):giab:
CLOSED: [2023-08-01 Tue 23:16] SCHEDULED: <202 3-08-02 Wed>
https://www.twistbioscience.com/resources/data-files/ngs-human-core-exome-panel-bed-file
#+begin_src
nextflow run workflows/compareVCF.nf -profile standard,helios --query=out/2300346867_63118093_NA12878-GRCh38/callVariant/haplotypecaller/2300346867_63118093_NA12878-GRCh38.vcf.gz --outdir=out/2300346867_63118093_NA12878-GRCh38/happy-twist-exome-core/ --compare=happy -lib lib --capture=capture/Twist_Exome_Core_Covered_Targets_hg38.bed  --id=HG001 --genome=GRCh38 -bg
#+end_src
| Type  | Filter | TRUTH.TOTAL | TRUTH.TP | TRUTH.FN | QUERY.TOTAL | QUERY.FP | QUERY.UNK | FP.gt | FP.al | METRIC.Recall | METRIC.Precision | METRIC.Frac_NA | METRIC.F1_Score | TRUTH.TOTAL.TiTv_ratio | QUERY.TOTAL.TiTv_ratio | TRUTH.TOTAL.het_hom_ratio | QUERY.TOTAL.het_hom_ratio |
| INDEL | ALL    |         328 |      313 |       15 |         722 |       95 |       309 |     4 |    13 |      0.954268 |         0.769976 |       0.427978 |        0.852273 |                        |                        |        1.8584070796460177 |        2.8967391304347827 |
| INDEL | PASS   |         328 |      313 |       15 |         722 |       95 |       309 |     4 |    13 |      0.954268 |         0.769976 |       0.427978 |        0.852273 |                        |                        |        1.8584070796460177 |        2.8967391304347827 |
| SNP   | ALL    |       19198 |    18962 |      236 |       23381 |      684 |      3738 |    48 |    10 |      0.987707 |         0.965178 |       0.159873 |        0.976313 |     3.1034188034188035 |      2.859264147830391 |        1.5669565217391304 |        1.8578767123287672 |
| SNP   | PASS   |       19198 |    18962 |      236 |       23381 |      684 |      3738 |    48 |    10 |      0.987707 |         0.965178 |       0.159873 |        0.976313 |     3.1034188034188035 |      2.859264147830391 |        1.5669565217391304 |        1.8578767123287672 |
**** DONE Test Twist Human core Exome (hg38):giab:
CLOSED: [2023-08-05 Sat 09:25] SCHEDULED: <2023-08-03 Thu 20:00>
#+begin_src sh
ID="2300346867_NA12878-63118093_S260-GRCh38"; nextflow run workflows/compareVCF.nf -profile standard,helios --query=out/${ID}/callVariant/haplotypecaller/${ID}.vcf.gz --outdir=out/${ID}/happy-twist-exome-core/ --compare=happy -lib lib --capture=capture/Twist_Exome_Core_Covered_Targets_hg38.bed  --id=HG001 --genome=GRCh38 -bg
#+end_src
**** DONE Tester Agilen SureSelect All Exon V8 (hg38) GATK-4.4:giab:
CLOSED: [2023-08-05 Sat 09:25] SCHEDULED: <2023-08-03 Thu 20:00>
**** DONE Vérifier l'impact gatk 4.3 - 4.4 : aucun
CLOSED: [2023-08-05 Sat 09:25]
**** DONE Figure comparant les 3 capture :hg001:
CLOSED: [2023-08-06 Sun 20:24] SCHEDULED: <2023-08-06 Sun>
**** DONE Mail Paul sur  les 3 capture :hg001:
CLOSED: [2023-08-06 Sun 20:24] SCHEDULED: <2023-08-06 Sun>
**** KILL Tester si le panel Twist Alliance VCGS Exome suffit
CLOSED: [2023-07-31 Mon 22:31] SCHEDULED: <2023-07-30 Sun>
**** DONE Mail cento pour demande le type de capture
CLOSED: [2023-10-07 Sat 17:59]
/Entered on/ [2023-08-07 Mon 20:40]
Twist exome
*** PROJ Comparer happy et happy-vcfeval :giab:
** TODO Données CHM13 :chm:
https://github.com/lh3/CHM-eval
*** TODO Run ERR1341793
SCHEDULED: <2023-10-29 Sun>
(raw reads ERR1341793_1.fastq.gz and ERR1341793_2.fastq.gz downloaded from https://www.ebi.ac.uk/ena/browser/view/ERR1341793)
*** TODO Run ERR1341796
SCHEDULED: <2023-10-29 Sun>
** TODO Insilico :cento:
*** TODO tous les variants centogène
**** DONE Extraire liste des SNVs
CLOSED: [2023-04-22 Sat 17:32] SCHEDULED: <2023-04-17 Mon>
***** DONE Corriger manquant à la main
CLOSED: [2023-04-22 Sat 17:31]
La sortie est sauvegardé dans git-annex : variants_success.csv
***** DONE Automa

Replacement in projects/bisonex.org at line 79 [5.35]

B:BD[9.43661] → [2.16828:27828]

 from summarising data in this way. "
**** DONE Mail alexis
CLOSED: [2023-08-20 Sun 13:45] SCHEDULED: <2023-08-20 Sun>
**** TODO Données simuscop 200x
SCHEDULED: <2023-10-22 Sun>
**** DONE En T2T avec liftover (filtre = spip) : ok mais lent et trop de variants :tests:
CLOSED: [2023-09-17 Sun 17:13] SCHEDULED: <2023-09-17 Sun>
1. Conversion en bed
#+begin_src sh :dir:~/code/sanger
open snvs-cento-sanger.csv | select chrom pos | insert pos2 {$in.pos } | to csv --separator="\t" | save snvs-cento-sanger.bed -f
#+end_src
2. Liftover avec UCSC (en ligne)
NB: vérifié sur le premier résultat en cherche le read contenant le variant (samtools view -r puis samtools view | grep en T2T) et avec l'aide d'IGV, on a un variant qui correspond en
chr1:10757746
3. En supposant que l'ordre des variants n'a pas changé, on ajoute simplement REF et ALT avec annotateLifted.jl
Annotation spip *très lente* : 1h13 !
Résultat:
2×3 DataFrame
 Row │ variant              meanQual  depth
     │ String               Float64   Int64
─────┼──────────────────────────────────────
   1 │ chr12:g.13594572      60.0      1
   2 │ chr17:g.10204026      60.0      1
144 found over 146
filter depth : another 0 missed variants
filter poly : another 0 missed variants
filter vep   : another 0 missed variants
Et on a trop de variants en sortie (7330 !)
**** DONE Mail Paul avec résultats filtre en T2T + nouveau schéma
CLOSED: [2023-09-17 Sun 23:15] SCHEDULED: <2023-09-17 Sun>
** TODO Medically relevant genes
SCHEDULED: <2023-10-25 Wed>
/Entered on/ [2023-10-18 Wed 22:37]
* Ré-interprétation :reanalysis:
** DONE Lancer tests sur données brutes [225/250] <(samples.csv)>  <(runs.waiting)>
CLOSED: [2023-10-14 Sat 11:58] SCHEDULED: <2023-10-08 Sun>
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- [X] 2200550471_63020031
- [X] 2200550490_63019351
- [X] 2200550505_63019340
- [X] 2200555565_63018614
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- [X] 2200570001_63021580
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- [X] 2200570042_63021493
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- [X] 2200579897_63024910
- [X] 2200583995_63024866
- [X] 2200584035_63024905
- [X] 2200584069_63024888
- [X] 2200584126_63024810
- [X] 2200589507_63026712
- [X] 2200597365_63027994
- [X] 2200597480_63027988
- [X] 2200597752_63026853
- [X] 2200597778_63027992
- [X] 22005977_63026903
- [X] 2200609031_63026527
- [X] 2200614198_63113928
- [X] 2200620372_63030821
- [X] 2200620442_63030810
- [X] 2200620498_63030816
- [X] 2200620628_63031031
- [X] 2200622310_63030984
- [X] 2200622355_63030956
- [X] 2200625369_63028699
- [X] 2200625410_63028697
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- [X] 2200635149_63033182
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- [X] 2200650089_63038093
- [X] 2200666292_63076568
- [X] 2200669188_63036688
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- [X] 2200694917_63042696
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- [X] 2200699345_63040238
- [X] 2200699383_63043050
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- [X] 220071551_63048935
- [X] 2200731515_63048963
- [X] 2200748145_63051198
- [X] 2200748171_63051213
- [X] 2200751046_63051249
- [X] 2200751101_63051234
- [X] 2200766471_63054590
- [X] 2200767731_63054595
- [X] 2200767822_63054464
- [X] 2200775505_63060410
- [X] 2200850441_63019345
- [X] 220597589_63026879
- [X] 2300003253_63060430
- [X] 2300005679_63060370
- [X] 2300009914_63060390
- [X] 2300028784_63060001
- [X] 2300036815_63063357
- [X] 2300055382_63061874
- [X] 2300055421_63061871
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- [X] 2300071111_63070356
- [X] 2300083434_63071675
- [X] 2300103609_63076239
- [X] 2300104572_63076232
- [X] 2300109602_63076765
- [X] 2300109665_63076770
- [X] 2300119721_63078732
- [X] 2300137773_63078133
- [X] 2300137834_63078123
- [X] 2300167821_63086183
- [X] 2300172698_63113453
- [X] 2300188216_63090609
- [X] 2300188281_63090632
- [ ] 2300188800_63090616
- [ ] 2300193193645_63090623
- [ ] 2300193668_63090611
- [ ] 2300195426_63090608
- [ ] 2300201017_63089636
- [ ] 2300227479_63098330
- [ ] 2300232688_63130821
- [ ] 2300292749_63109239
- [ ] 230029277_63109247
- [ ] 2300294712_63109236
- [ ] 2300308032_63111581
- [ ] 2300323537_63114209
- [ ] 2300334609_63115535
- [ ] 2300346867_63118093
- [ ] 2300346867_63118093_NA12878
- [ ] 2300348940_63118099
- [ ] 2300359806_63119915
- [ ] 2300380476_63123963
- [ ] 2300382582_63123749
- [ ] 2300384269_63126867
- [ ] 2300407581_63130826
- [ ] 2300407626_63130842
- [ ] 2300409593_63130874
- [ ] 2300409612_63130980
- [ ] 2300417623_63131524
** 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 Comparer variants cento à sortie bisonex :checkpipeline:
SCHEDULED: <2023-10-21 Sat>
*** TODO Ajouter négatifs dans la liste des variants
SCHEDULED: <2023-10-21 Sat>
*** TODO Mettre à jour liste des variants
SCHEDULED: <2023-10-21 Sat>
*** KILL Lifter coordonées variants cento génomique en GRCh38
CLOSED: [2023-10-21 Sat 22:47]
*** TODO Un seul exécutable pour toutes les étapes
SCHEDULED: <2023-10-21 Sat>
Un utilitaire en ligne de commande qui appel les différentes étapes.
On utilise une structure unique pour toutes les étapes mais qui sera remplie au fur et à mesure. En stockant dans un csv à chaque étape
**** DONE parse variants
CLOSED: [2023-10-21 Sat 23:29] SCHEDULED: <2023-10-21 Sat>
**** TODO Un seul type de données
SCHEDULED: <2023-10-21 Sat>
**** TODO annote avec mobidetails
SCHEDULED: <2023-10-21 Sat>
**** TODO compare chaque variant avec la sortie du pipeline
SCHEDULED: <2023-10-21 Sat>
**** TODO confirme ou non en Sanger
SCHEDULED: <2023-10-21 Sat>
* 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]

[9.43661]

 from summarising data in this way. "
**** DONE Mail alexis
CLOSED: [2023-08-20 Sun 13:45] SCHEDULED: <2023-08-20 Sun>
**** TODO Données simuscop 200x
SCHEDULED: <2023-10-29 Sun>
**** DONE En T2T avec liftover (filtre = spip) : ok mais lent et trop de variants :tests:
CLOSED: [2023-09-17 Sun 17:13] SCHEDULED: <2023-09-17 Sun>
1. Conversion en bed
#+begin_src sh :dir:~/code/sanger
open snvs-cento-sanger.csv | select chrom pos | insert pos2 {$in.pos } | to csv --separator="\t" | save snvs-cento-sanger.bed -f
#+end_src
2. Liftover avec UCSC (en ligne)
NB: vérifié sur le premier résultat en cherche le read contenant le variant (samtools view -r puis samtools view | grep en T2T) et avec l'aide d'IGV, on a un variant qui correspond en
chr1:10757746
3. En supposant que l'ordre des variants n'a pas changé, on ajoute simplement REF et ALT avec annotateLifted.jl
Annotation spip *très lente* : 1h13 !
Résultat:
2×3 DataFrame
 Row │ variant              meanQual  depth
     │ String               Float64   Int64
─────┼──────────────────────────────────────
   1 │ chr12:g.13594572      60.0      1
   2 │ chr17:g.10204026      60.0      1
144 found over 146
filter depth : another 0 missed variants
filter poly : another 0 missed variants
filter vep   : another 0 missed variants
Et on a trop de variants en sortie (7330 !)
**** DONE Mail Paul avec résultats filtre en T2T + nouveau schéma
CLOSED: [2023-09-17 Sun 23:15] SCHEDULED: <2023-09-17 Sun>
** TODO Medically relevant genes
SCHEDULED: <2023-10-25 Wed>
/Entered on/ [2023-10-18 Wed 22:37]
* Ré-interprétation :reanalysis:
** DONE Lancer tests sur données brutes [225/250] <(samples.csv)>  <(runs.waiting)>
CLOSED: [2023-10-14 Sat 11:58] SCHEDULED: <2023-10-08 Sun>
- [X] 100222_63015289
- [X] 1600304839_63051311
- [X] 1900007827_62913191
- [X] 1900398899_62999500
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- [X] 2200609031_63026527
- [X] 2200614198_63113928
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- [X] 2200620442_63030810
- [X] 2200620498_63030816
- [X] 2200620628_63031031
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- [X] 2200680342_63105271
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- [X] 2200694858_63042702
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- [X] 2200731515_63048963
- [X] 2200748145_63051198
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- [X] 2200767731_63054595
- [X] 2200767822_63054464
- [X] 2200775505_63060410
- [X] 2200850441_63019345
- [X] 220597589_63026879
- [X] 2300003253_63060430
- [X] 2300005679_63060370
- [X] 2300009914_63060390
- [X] 2300028784_63060001
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- [X] 230006894_63064950
- [X] 2300071111_63070356
- [X] 2300083434_63071675
- [X] 2300103609_63076239
- [X] 2300104572_63076232
- [X] 2300109602_63076765
- [X] 2300109665_63076770
- [X] 2300119721_63078732
- [X] 2300137773_63078133
- [X] 2300137834_63078123
- [X] 2300167821_63086183
- [X] 2300172698_63113453
- [X] 2300188216_63090609
- [X] 2300188281_63090632
- [ ] 2300188800_63090616
- [ ] 2300193193645_63090623
- [ ] 2300193668_63090611
- [ ] 2300195426_63090608
- [ ] 2300201017_63089636
- [ ] 2300227479_63098330
- [ ] 2300232688_63130821
- [ ] 2300292749_63109239
- [ ] 230029277_63109247
- [ ] 2300294712_63109236
- [ ] 2300308032_63111581
- [ ] 2300323537_63114209
- [ ] 2300334609_63115535
- [ ] 2300346867_63118093
- [ ] 2300346867_63118093_NA12878
- [ ] 2300348940_63118099
- [ ] 2300359806_63119915
- [ ] 2300380476_63123963
- [ ] 2300382582_63123749
- [ ] 2300384269_63126867
- [ ] 2300407581_63130826
- [ ] 2300407626_63130842
- [ ] 2300409593_63130874
- [ ] 2300409612_63130980
- [ ] 2300417623_63131524
** 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 Comparer variants cento à sortie bisonex :checkpipeline:
SCHEDULED: <2023-10-21 Sat>
*** TODO Un seul exécutable pour toutes les étapes
SCHEDULED: <2023-10-21 Sat>
Un utilitaire en ligne de commande qui appel les différentes étapes.
On utilise une structure unique pour toutes les étapes mais qui sera remplie au fur et à mesure. En stockant dans un csv à chaque étape
**** DONE parse variants
CLOSED: [2023-10-21 Sat 23:29] SCHEDULED: <2023-10-21 Sat>
**** DONE Ajouter négatifs dans la liste des variants
CLOSED: [2023-10-22 Sun 23:01] SCHEDULED: <2023-10-21 Sat>
**** DONE Mettre à jour liste des variants
CLOSED: [2023-10-22 Sun 23:01] SCHEDULED: <2023-10-21 Sat>
- [X] Régéner la liste des variants
- [ ] Retrouver les variants modifié à la main avec diff
On ne garde que les ajouts
#+begin_src sh
awk -F ',' '{print $1","$2":"$3$4$5}' extracted.csv | ^sort | save -f extracted_concat.csv
xsv select 1-2 ~/annex/data/centogene/variants/variant_genomic.csv  | ^sort | save variant_genomic_corr.csv -f
diff extracted_concat.csv variant_genomic_corr.csv  | grep '^>' | save -f update.diff
#+end_src
- [X] Ajouter négatifs
345 variants non trouvés avant modification
141 après modification
- [X] Ajouter différence
- [X] Corriger erreurs de parsing
**** KILL Lifter coordonées variants cento génomique en GRCh38
CLOSED: [2023-10-21 Sat 22:47]
**** TODO Un seul type de données
SCHEDULED: <2023-10-21 Sat>
**** TODO variant_recoder pour avoir les coordonnées VCF
SCHEDULED: <2023-10-21 Sat>
**** TODO compare chaque variant avec la sortie du pipeline
SCHEDULED: <2023-10-21 Sat>
**** TODO confirme ou non en Sanger
SCHEDULED: <2023-10-21 Sat>
* Résultats
** TODO Speed-up BWA-mem
SCHEDULED: <2023-10-29 Sun>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-10-29 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]