apraga/org - Change YYWM6OI2VFDS6F3CF3D22NRB6CZQBRCTQQJUESXDBBN73PA443WAC

Bisonex: download T2T

Created by Alexis Praga on June 12, 2023

YYWM6OI2VFDS6F3CF3D22NRB6CZQBRCTQQJUESXDBBN73PA443WAC

Dependencies

In channels

main

Change contents

Insertion in workout.org at line 6353 [4.1]
[2.131]
```
* <2023-06-13 Tue> Workout
 Circuit 3x3 !!
```

Replacement in projects/bisonex.org at line 3 [5.35]

B:BD[3.8221] → [3.8221:16039]

∅:D[3.16039] → [6.16413:16787]

B:BD[6.16413] → [6.16413:16787]

 (avec le fichier gff)
  On utilise la version chromosome donc on annote dbSNP (à faire)
** Performances
Ordinateur de Carine (WSL2) : 4h dont 1h15 alignement (parallélisé) et 1h15 haplotypecaller (séquentiel)
** Chromosomes NC, NT, NW
Correspondance :
https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&chromInfoPage=
Signification
https://genome.ucsc.edu/FAQ/FAQdownloads.html#downloadAlt
- alt = séquences alternatives (utilisables)
- fix = patch (correction ou amélioration)
- random = séquence connue sur un chromosome mais non encore utilisée
** Pipelines prêt-à-l’emploi nextflow
Problème : nécessite singularity ou docker (ou conda)
Potentiellement utilisable avec nix...
** Validation : Quelles données de référence ?
Discussion avec Alexis
- Platinum genomes = génome seul
*** [[https://github.com/genome-in-a-bottle/giab_data_indexes][Genome in a bottle]]
  - NA12878 :
    - Illumina HiSeq Exome : fastq + capture
    - Illumina TruSeq Exome : bam, pas de capture
      ici ww
  - HG002,3,4
    - Illumina Whole Exome  : bam. le kit de capture est "Agilent SureSelect Human All Exon V5 kit" selon [[https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/OsloUniversityHospital_Exome_GATK_jointVC_11242015/README.txt][README]]. On il faut les régions [[https://kb.10xgenomics.com/hc/en-us/articles/115004150923-Where-can-I-find-the-Agilent-Target-BED-files-][selon ce site]]
      Un autre fichier est disponible (capture ???)
    https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/OsloUniversityHospital_Exome_GATK_jointVC_11242015/wex_Agilent_SureSelect_v05_b37.baits.slop50.merged.list
  "target region" +/- 50bp
    testé sur chr311780-312086 : ok
Autres technologies non adaptées au pipeline (vu avec Alexis)
*** [[https://www.illumina.com/platinumgenomes.html][Platinum genome
]] Que du génome « sequenced to 50x depth on a HiSeq 2000 system”
Genome possible
** Zone de capture
GIAB fourni le .bed pour l'exome . INfo : https://support.illumina.com/sequencing/sequencing_kits/nextera-rapid-capture-exome-kit/downloads.html
** Centogène
https://www.twistbioscience.com/node/23906
Bed non fourni pour exactement cette capture
On prend https://www.twistbioscience.com/resources/data-files/twist-alliance-vcgs-exome-401mb-bed-files
qui content la majeure partie
* Données :data:
** DONE Remplacer bam par fastq sur mesocentre
CLOSED: [2023-04-16 Sun 16:33]
Commande
*** DONE Supprimer les fastq non "paired"
CLOSED: [2023-04-16 Sun 16:33]
nushell
Liste des fastq avec "paired-end" manquant
#+begin_src nu
ls **/*.fastq.gz | get name | path basename | split column "_" | get column1 | uniq -u | save single.txt
#+end_src
#+RESULTS:
: 62907927
: 62907970
: 62899606
: 62911287
: 62913201
: 62914084
: 62915905
: 62921595
: 62923065
: 62925220
: 62926503
: 62926502
: 62926500
: 62926499
: 62926498
: 62931719
: 62943423
: 62943400
: 62948290
: 62949205
: 62949206
: 62949118
: 62951284
: 62960792
: 62960785
: 62960787
: 62960617
: 62962561
: 62962692
: 62967473
: 62972194
: 62979102
On vérifie
#+begin_src nu
open single.txt  | lines | each {|e| ls $"fastq/*_($in)/*" | get 0  }
open single.txt  | lines | each {|e| ls $"fastq/*_($in)/*" | get 0.name }  | path basename | split column "_" | get column1 | uniq -c
#+end_src
On met tous dans un dossier (pas de suppression )
#+begin_src
open single.txt  | lines | each {|e| ls $"fastq/*_($in)/*" | get 0  }  | each {|e| ^mv $e.name bad-fastq/}
#+end_src
On vérifie que les dossiier sont videsj
 open single.txt  | lines | each {|e| ls $"fastq/*_($in)" | get 0.name } | ^ls -l $in
 Puis on supprime
 open single.txt  | lines | each {|e| ls $"fastq/*_($in)" | get 0.name } | ^rm -r $in
*** DONE Supprimer bam qui ont des fastq
CLOSED: [2023-04-16 Sun 16:33]
On liste les identifiants des fastq et bam dans un tableau avec leur type :
#+begin_src
let fastq = (ls fastq/*/*.fastq.gz | get name | parse "{dir}/{full_id}/{id}_{R}_001.fastq.gz"  | select dir id | uniq )
let bam = (ls bam/*/*.bam | get name | parse "{dir}/{full_id}/{id}_{S}.bqrt.bam"  | select dir id)
#+end_src
On groupe les résultat par identifiant (résultats = liste de records qui doit être convertie en table)
et on trie ceux qui n'ont qu'un fastq ou un bam
#+begin_src
let single = ( $bam | append $fastq | group-by id | transpose id files | get files | where {|x| ($x | length) == 1})
#+end_src
On convertit en table et on récupère seulement les bam
#+begin_src
$single | reduce {|it, acc| $acc | append $it} | where dir == bam | get id | each {|e| ^ls $"bam/*_($e)/*.bam"}
#+end_src
#+RESULTS:
: bam/2100656174_62913201/62913201_S52.bqrt.bam
: bam/2100733271_62925220/62925220_S33.bqrt.bam
: bam/2100738763_62926502/62926502_S108.bqrt.bam
: bam/2100746726_62926498/62926498_S105.bqrt.bam
: bam/2100787936_62931955/62931955_S4.bqrt.bam
: bam/2200066374_62948290/62948290_S130.bqrt.bam
: bam/2200074722_62948298/62948298_S131.bqrt.bam
: bam/2200074990_62948306/62948306_S218.bqrt.bam
: bam/2200214581_62967331/62967331_S267.bqrt.bam
: bam/2200225399_62972187/62972187_S85.bqrt.bam
: bam/2200293962_62979117/62979117_S63.bqrt.bam
: bam/2200423985_62999352/62999352_S1.bqrt.bam
: bam/2200495073_63010427/63010427_S20.bqrt.bam
: bam/2200511274_63012586/63012586_S114.bqrt.bam
: bam/2200669188_63036688/63036688_S150.bqrt.bam
* Nouveau workflow :workflow:
** TODO Bases de données
*** KILL Nix pour télécharger les données brutes
**** Conclusion
Non viable sur cluster car en dehors de /nix/store
On peut utiliser des symlink mais trop compliqué
**** KILL Axel au lieu de curl pour gérer les timeout?
CLOSED: [2022-08-19 Fri 15:18]
*** DONE Tester patch de @pennae pour gros fichiers
SCHEDULED: <2022-08-19 Fri>
*** STRT Télécharger les données avec nextflow
**** DONE Genome de référence
**** DONE dbSNP
**** TODO VEP 20G
Ajout vérification checksum -> à vérifier
**** TODO transcriptome (spip)
Rajouter checksum manuel
**** KILL Refseq
**** STRT OMIM
codé, à vérifier
**** TODO ACMG incidental
*** HOLD Processing bases de données
**** DONE dbSNP common
**** DONE Seulement les ID dans dbSNP common !
CLOSED: [2022-11-19 Sat 21:42]
172G au lieu de 253M...
**** HOLD common dbSNP not clinvar patho
***** DONE Conclusion partielle
CLOSED: [2022-12-12 Mon 22:25]
- vcfeval : prometteur mais n'arrive pas à traiter toutes les régions
- isec : trop de problèmes avec
- classif clinvar directement dans dbSNP: le plus simple
  Et ça permet de rattraper quelques erreurs dans le script d'Alexis
***** KILL Utiliser directement le numéro dbSNP dans clinvar ? Non
CLOSED: [2022-11-20 Sun 19:51]
Ex: chr20
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools query -f 'rs%INFO/RS \n' -i 'INFO/RS != "." & INFO/CLNSIG="Pathogenic"' clinvar_chr20.vcf.gz | sort > ID_clinvar_patho.txt
bcftools query -f '%ID\n' dbSNP_common_chr20.vcf.gz | sort > ID_of_common_snp.txt
comm -23 ID_of_common_snp.txt ID_clinvar_patho.txt > ID_of_common_snp_not_clinvar_patho.txt
wc -l ID_of_common_snp_not_clinvar_patho.txt
# sort ID
#+end_src
#+RESULTS:
: 518846 ID_of_common_snp_not_clinvar_patho.txt
Version d'alexis
#+begin_src sh :dir ~/code/bisonex/test_isec
snp=dbSNP_common_chr20.vcf.gz
clinvar=clinvar_chr20_notremapped.vcf.gz
python ../script/pythonScript/clinvar_sbSNP.py \
    --clinvar $clinvar \
    --chrm_name_table ../database/RefSeq/refseq_to_number_only_consensual.txt \
    --dbSNP $snp --output prod.txt
wc -l prod.txt
zgrep '^NC' dbSNP_common_chr20.vcf.gz | wc -l
#+end_src
#+RESULTS:
| 518832 | prod.txt |
| 518846 |          |
***** KILL classification clinvar codée dbSNP ?
CLOSED: [2022-12
-04 Sun 14:38]
Sur le chromosome 20
*Attention* CLNSIG a plusieurs champs (séparé par une virgule)
On y accède avec INFO/CLNSIG[*]
Ensuite, chaque item peut avoir plusieurs haploïdie (séparé par un |). IL faut donc utiliser une regexp
NB: *ne pas mettre la condition* dans une variable !!
Pour avoir les clinvar patho, on veut 5 mais pas 255 (= autre) pour la

[3.8221]

[7.16138]

 (avec le fichier gff)
  On utilise la version chromosome donc on annote dbSNP (à faire)
** Performances
Ordinateur de Carine (WSL2) : 4h dont 1h15 alignement (parallélisé) et 1h15 haplotypecaller (séquentiel)
** Chromosomes NC, NT, NW
Correspondance :
https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&chromInfoPage=
Signification
https://genome.ucsc.edu/FAQ/FAQdownloads.html#downloadAlt
- alt = séquences alternatives (utilisables)
- fix = patch (correction ou amélioration)
- random = séquence connue sur un chromosome mais non encore utilisée
** Pipelines prêt-à-l’emploi nextflow
Problème : nécessite singularity ou docker (ou conda)
Potentiellement utilisable avec nix...
** Validation : Quelles données de référence ?
Discussion avec Alexis
- Platinum genomes = génome seul
*** [[https://github.com/genome-in-a-bottle/giab_data_indexes][Genome in a bottle]]
  - NA12878 :
    - Illumina HiSeq Exome : fastq + capture
    - Illumina TruSeq Exome : bam, pas de capture
      ici ww
  - HG002,3,4
    - Illumina Whole Exome  : bam. le kit de capture est "Agilent SureSelect Human All Exon V5 kit" selon [[https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/OsloUniversityHospital_Exome_GATK_jointVC_11242015/README.txt][README]]. On il faut les régions [[https://kb.10xgenomics.com/hc/en-us/articles/115004150923-Where-can-I-find-the-Agilent-Target-BED-files-][selon ce site]]
      Un autre fichier est disponible (capture ???)
    https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/OsloUniversityHospital_Exome_GATK_jointVC_11242015/wex_Agilent_SureSelect_v05_b37.baits.slop50.merged.list
  "target region" +/- 50bp
    testé sur chr311780-312086 : ok
Autres technologies non adaptées au pipeline (vu avec Alexis)
*** [[https://www.illumina.com/platinumgenomes.html][Platinum genome
]] Que du génome « sequenced to 50x depth on a HiSeq 2000 system”
Genome possible
** Zone de capture
GIAB fourni le .bed pour l'exome . INfo : https://support.illumina.com/sequencing/sequencing_kits/nextera-rapid-capture-exome-kit/downloads.html
** Centogène
https://www.twistbioscience.com/node/23906
Bed non fourni pour exactement cette capture
On prend https://www.twistbioscience.com/resources/data-files/twist-alliance-vcgs-exome-401mb-bed-files
qui content la majeure partie
* Données :data:
** DONE Remplacer bam par fastq sur mesocentre
CLOSED: [2023-04-16 Sun 16:33]
Commande
*** DONE Supprimer les fastq non "paired"
CLOSED: [2023-04-16 Sun 16:33]
nushell
Liste des fastq avec "paired-end" manquant
#+begin_src nu
ls **/*.fastq.gz | get name | path basename | split column "_" | get column1 | uniq -u | save single.txt
#+end_src
#+RESULTS:
: 62907927
: 62907970
: 62899606
: 62911287
: 62913201
: 62914084
: 62915905
: 62921595
: 62923065
: 62925220
: 62926503
: 62926502
: 62926500
: 62926499
: 62926498
: 62931719
: 62943423
: 62943400
: 62948290
: 62949205
: 62949206
: 62949118
: 62951284
: 62960792
: 62960785
: 62960787
: 62960617
: 62962561
: 62962692
: 62967473
: 62972194
: 62979102
On vérifie
#+begin_src nu
open single.txt  | lines | each {|e| ls $"fastq/*_($in)/*" | get 0  }
open single.txt  | lines | each {|e| ls $"fastq/*_($in)/*" | get 0.name }  | path basename | split column "_" | get column1 | uniq -c
#+end_src
On met tous dans un dossier (pas de suppression )
#+begin_src
open single.txt  | lines | each {|e| ls $"fastq/*_($in)/*" | get 0  }  | each {|e| ^mv $e.name bad-fastq/}
#+end_src
On vérifie que les dossiier sont videsj
 open single.txt  | lines | each {|e| ls $"fastq/*_($in)" | get 0.name } | ^ls -l $in
 Puis on supprime
 open single.txt  | lines | each {|e| ls $"fastq/*_($in)" | get 0.name } | ^rm -r $in
*** DONE Supprimer bam qui ont des fastq
CLOSED: [2023-04-16 Sun 16:33]
On liste les identifiants des fastq et bam dans un tableau avec leur type :
#+begin_src
let fastq = (ls fastq/*/*.fastq.gz | get name | parse "{dir}/{full_id}/{id}_{R}_001.fastq.gz"  | select dir id | uniq )
let bam = (ls bam/*/*.bam | get name | parse "{dir}/{full_id}/{id}_{S}.bqrt.bam"  | select dir id)
#+end_src
On groupe les résultat par identifiant (résultats = liste de records qui doit être convertie en table)
et on trie ceux qui n'ont qu'un fastq ou un bam
#+begin_src
let single = ( $bam | append $fastq | group-by id | transpose id files | get files | where {|x| ($x | length) == 1})
#+end_src
On convertit en table et on récupère seulement les bam
#+begin_src
$single | reduce {|it, acc| $acc | append $it} | where dir == bam | get id | each {|e| ^ls $"bam/*_($e)/*.bam"}
#+end_src
#+RESULTS:
: bam/2100656174_62913201/62913201_S52.bqrt.bam
: bam/2100733271_62925220/62925220_S33.bqrt.bam
: bam/2100738763_62926502/62926502_S108.bqrt.bam
: bam/2100746726_62926498/62926498_S105.bqrt.bam
: bam/2100787936_62931955/62931955_S4.bqrt.bam
: bam/2200066374_62948290/62948290_S130.bqrt.bam
: bam/2200074722_62948298/62948298_S131.bqrt.bam
: bam/2200074990_62948306/62948306_S218.bqrt.bam
: bam/2200214581_62967331/62967331_S267.bqrt.bam
: bam/2200225399_62972187/62972187_S85.bqrt.bam
: bam/2200293962_62979117/62979117_S63.bqrt.bam
: bam/2200423985_62999352/62999352_S1.bqrt.bam
: bam/2200495073_63010427/63010427_S20.bqrt.bam
: bam/2200511274_63012586/63012586_S114.bqrt.bam
: bam/2200669188_63036688/63036688_S150.bqrt.bam
* Nouveau workflow :workflow:
** TODO Bases de données
*** KILL Nix pour télécharger les données brutes
**** Conclusion
Non viable sur cluster car en dehors de /nix/store
On peut utiliser des symlink mais trop compliqué
**** KILL Axel au lieu de curl pour gérer les timeout?
CLOSED: [2022-08-19 Fri 15:18]
*** DONE Tester patch de @pennae pour gros fichiers
SCHEDULED: <2022-08-19 Fri>
*** KILL Télécharger les données avec nextflow: hg38
CLOSED: [2023-06-12 Mon 23:29]
**** DONE Genome de référence
**** DONE dbSNP
**** DONE VEP 20G
CLOSED: [2023-06-12 Mon 23:29]
Ajout vérification checksum -> à vérifier
**** DONE transcriptome (spip)
CLOSED: [2023-06-12 Mon 23:29]
Rajouter checksum manuel
**** KILL Refseq
**** KILL OMIM
CLOSED: [2023-06-12 Mon 23:29]
codé, à vérifier
**** KILL ACMG incidental
CLOSED: [2023-06-12 Mon 23:29]
*** TODO Télécharge données :TIT:
SCHEDULED: <2023-06-15 Thu>
**** DONE fasta
CLOSED: [2023-06-12 Mon 23:30]
**** DONE fasta : compatibilité hg38
CLOSED: [2023-06-12 Mon 23:30]
**** DONE fasta index
CLOSED: [2023-06-13 Tue 00:07]
**** DONE fasta index: compatibilité hg38
CLOSED: [2023-06-13 Tue 00:07]
**** DONE fasta dictionnaire
CLOSED: [2023-06-13 Tue 00:07]
**** DONE dbSNP
CLOSED: [2023-06-12 Mon 23:30]
**** DONE dbSNP : compatibilité hg38
CLOSED: [2023-06-12 Mon 23:30]
*** HOLD Processing bases de données
**** DONE dbSNP common
**** DONE Seulement les ID dans dbSNP common !
CLOSED: [2022-11-19 Sat 21:42]
172G au lieu de 253M...
**** HOLD common dbSNP not clinvar patho
***** DONE Conclusion partielle
CLOSED: [2022-12-12 Mon 22:25]
- vcfeval : prometteur mais n'arrive pas à traiter toutes les régions
- isec : trop de problèmes avec
- classif clinvar directement dans dbSNP: le plus simple
  Et ça permet de rattraper quelques erreurs dans le script d'Alexis
***** KILL Utiliser directement le numéro dbSNP dans clinvar ? Non
CLOSED: [2022-11-20 Sun 19:51]
Ex: chr20
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools query -f 'rs%INFO/RS \n' -i 'INFO/RS != "." & INFO/CLNSIG="Pathogenic"' clinvar_chr20.vcf.gz | sort > ID_clinvar_patho.txt
bcftools query -f '%ID\n' dbSNP_common_chr20.vcf.gz | sort > ID_of_common_snp.txt
comm -23 ID_of_common_snp.txt ID_clinvar_patho.txt > ID_of_common_snp_not_clinvar_patho.txt
wc -l ID_of_common_snp_not_clinvar_patho.txt
# sort ID
#+end_src
#+RESULTS:
: 518846 ID_of_common_snp_not_clinvar_patho.txt
Version d'alexis
#+begin_src sh :dir ~/code/bisonex/test_isec
snp=dbSNP_common_chr20.vcf.gz
clinvar=clinvar_chr20_notremapped.vcf.gz
python ../script/pythonScript/clinvar_sbSNP.py \
    --clinvar $clinvar \
    --chrm_name_table ../database/RefSeq/refseq_to_number_only_consensual.txt \
    --dbSNP $snp --output prod.txt
wc -l prod.txt
zgrep '^NC' dbSNP_common_chr20.vcf.gz | wc -l
#+end_src
#+RESULTS:
| 518832 | prod.txt |
| 518846 |          |
***** KILL classification clinvar codée dbSNP ?
CLOSED: [2022-12-04 Sun 14:38]
Sur le chromosome 20
*Attention* CLNSIG a plusieurs champs (séparé par une virgule)
On y accède avec INFO/CLNSIG[*]
Ensuite, chaque item peut avoir plusieurs haploïdie (séparé par un |). IL faut donc utiliser une regexp
NB: *ne pas mettre la condition* dans une variable !!
Pour avoir les clinvar patho, on veut 5 mais pas 255 (= autre) pour la

Replacement in projects/bisonex.org at line 47 [5.35]

B:BD[3.109094] → [3.109094:114036]

∅:D[3.114036] → [6.89338:91105]

B:BD[6.89338] → [6.89338:91105]

∅:D[6.91105] → [8.40819:41543]

B:BD[8.40819] → [8.40819:41543]

∅:D[9.8219] → [10.18704:19463]

∅:D[8.41543] → [10.18704:19463]

B:BD[10.18704] → [10.18704:19463]

SED: [2023-05-29 Mon 15:36]
****** DONE 1 SNV  : ok !
CLOSED: [2023-05-20 Sat 19:35] SCHEDULED: <2023-05-20 Sat>
#+begin_src
 make run READS="tests/bamscissors/corrected_{1,2}.fq.gz"
Puis on lance le pipeline sur correct_1
- [X] Variant visible dans IGV
- [X] Variant visible après alignement
- [X] Variant visible après appel de variant
****** KILL Tester SNV chromosome 22
CLOSED: [2023-05-29 Mon 15:36] SCHEDULED: <2023-05-20 Sat>
***** TODO PHase 2 : chr22, VAF variable
SCHEDULED: <2023-06-03 Sat>
****** DONE de nombreux reads sont perdus -> ok sur un SNV en alignant sur chromosome 22
CLOSED: [2023-05-29 Mon 15:38]
Problème dansr le BAM car sans les insertion
******* DONE Filtrer les reads sans pair : idem
CLOSED: [2023-05-23 Tue 00:01]
FOUND:Found 16662 unpaired mates
	at htsjdk.samtools.SAMUtils.processValidationError(SAMUtils.java:470)
	at picard.sam.SamToFastq.doWork(SamToFastq.java:224)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
ex: chr22:42213078
On essaie
samtools view ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135.bam NC_000022.11  -hf 0x2 -o 63003856_chr22.bam
Ne rale pas...
SCHEDULED: <2023-05-22 Mon>
******* DONE Problème de la conversion BAM -> fastq ?
CLOSED: [2023-05-24 Wed 23:19]
******** DONE Test bamtofastq sur le BAM originel: idem
CLOSED: [2023-05-23 Tue 01:16]
Dans ~/recherche/code/bisonex/Bamscissors.jl
samtools view ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135.bam NC_000022.11  -hf 0x2 -o 63003856_chr22.bam
On trie bien par nom de read
samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorted.bam
Conversion en fastq. Attention à bien prendre le *fichier trié* !
samtools bam2fq  -1 63003856_chr22_init1.fq.gz -2 63003856_chr22_init2.fq.gz  -n 63003856_chr22_sorted.bam
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 2592110 reads
On envoie sur le mésocentre
scp 63003856_chr22_init{1,2}.fq.gz meso:/Work/Users/apraga/bisonex/tests/bamscissors
On démarre un job avec 24 coeurs pour aller vite
srun -c 24 -p smp -t 1:00:00 --pty bash
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef 63003856_chr22_init1.fq.gz 63003856_chr22_init2.fq.gz | samtools sort -@24 -o output.bam -
Dans /home/alex/recherche/bisonex/code/BamScissors.jl/aligned
❯ scp meso:/Work/Users/apraga/bisonex/tests/bamscissors/output.bam*
******** DONE Avec samtools fastq
CLOSED: [2023-05-23 Tue 01:16]
samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorted.bam
samtools fastq 63003856_chr22_1.fq.gz -2 63003856_chr22_2.fq.gz -0 /dev/null -s /dev/null -o 63003856_chr22_sorted.bam
scp 63003856_chr22_{1,2}.fq.gz  meso:/Work/Users/apraga/bisonex/tests/bamscissors/
mesocentre
 bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef 63003856_chr22_1.fq.gz 63003856_chr22_2.fq.gz | samtools sort -@24 -o output.bam
 scp meso:/Work/Users/apraga/bisonex/tests/bamscissors/output.bam\* aligned/
******** DONE En rajoutant .fna dans le doserrie (+samtools fastq): idem
CLOSED: [2023-05-23 Tue 01:16]
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef* .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef* .
bwa mem -t 24 genomeRef 63003856_chr22_1.fq.gz 63003856_chr22_2.fq.gz | samtools sort -@24 -o output.bam
******** DONE Test picard : idem
CLOSED: [2023-05-23 Tue 01:16]
Dans bisonex/code/BamScissors.jl
❯ picard SamToFastq -I 63003856_chr22_sorted.bam -F testpicard1.fastq -F2 testpicard2.fastq
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef testpicard1.fastq.gz testpicard2.fastq.gz | samtools sort -@24 -o testpicard.bam -
******** DONE Il ne manque pas des reads dans les fastq :
CLOSED: [2023-05-23 Tue 01:26]
bisonex/code/BamScissors.jl on  bamscissors [!?] via ஃ v1.9.0
❯ samtools  flagstat aligned/output.bam
1306273 + 0 in total (QC-passed reads + QC-failed reads)
1296055 + 0 primary
0 + 0 secondary
10218 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
1304871 + 0 mapped (99.89% : N/A)
1294653 + 0 primary mapped (99.89% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
bisonex/code/BamScissors.jl on  bamscissors [!?] via ஃ v1.9.0
❯ samtools flagstat 63003856_chr22.bam
2609214 + 0 in total (QC-passed reads + QC-failed reads)
2592110 + 0 primary
0 + 0 secondary
17104 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
2609214 + 0 mapped (100.00% : N/A)
2592110 + 0 primary mapped (100.00% : N/A)
2592110 + 0 paired in sequencing
1296055 + 0 read1
1296055 + 0 read2
2592110 + 0 properly paired (100.00% : N/A)
2592110 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
❯ echo $(zcat 63003856_chr22_init2.fq.gz | wc -l)/4 | bc
1296055
bisonex/code/BamScissors.jl on  bamscissors [!?] via ஃ v1.9.0 took 2s
❯ echo $(zcat 63003856_chr22_init1.fq.gz | wc -l)/4 | bc
1296055
❯ samtools  flagstat 63003856_chr22_sorted.bam
2609214 + 0 in total (QC-passed reads + QC-failed reads)
2592110 + 0 primary
0 + 0 secondary
17104 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
2609214 + 0 mapped (100.00% : N/A)
2592110 + 0 primary mapped (100.00% : N/A)
2592110 + 0 paired in sequencing
1296055 + 0 read1
1296055 + 0 read2
2592110 + 0 properly paired (100.00% : N/A)
2592110 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
******** DONE Avec sort -O BAM idem
CLOSED: [2023-05-23 Tue 01:21]
******** DONE Singleton ou non mapped ? nonVirtPosition
CLOSED: [2023-05-23 Tue 01:22]
❯ samtools bam2fq  -1 63003856_chr22_init1.fq.gz -2 63003856_chr22_init2.fq.gz -0 both -s single.fq.gz  -n 63003856_chr22_sorted.bam
bisonex/code/BamScissors.jl on  bamscissors [!?] via ஃ v1.9.0
❯ wc -l 63003856_chr22_init* both single.fq.gz
   403540 63003856_chr22_init1.fq.gz
   404788 63003856_chr22_init2.fq.gz
        0 both
        0 single.fq.gz
   808328 total
******** Problème d'aligner car les reads sont bien dans le .fastq ?
Ex:
 zgrep "A00853:477:HMLWYDSX3:2:2624:2826:18630" 6300385
6_chr22_{1,2}.fq.gz
63003856_chr22_1.fq.gz:@A00853:477:HMLWYDSX3:2:2624:2826:18630
63003856_chr22_2.fq.gz:@A00853:477:HMLWYDSX3:2:2624:2826:18630
******* DONE Refaire la manip sur bam chr22 non modifié + mail Alexis
CLOSED: [2023-05-23 Tue 23:27]
[1]_samtools view ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135.bam NC_000022.11  -f 0x2 -o 63003856_chr22.bam
 Les reads sont bien tous mappé
samtools flagstat 63003856_chr22.bam
2609214 + 0 in total (QC-passed reads + QC-failed reads)
2592110 + 0 primary
0 + 0 secondary
17104 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
2609214 + 0 mapped (100.00% : N/A)
[2] samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorte
d.bam
flagstat idem
[3] samtools fastq -1 63003856_chr22_1.fq.gz -2 63003856_chr22_2.fq.gz -0 /dev/null -s /dev/null -n 63003856_chr22_sorted.bam
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 2592110 reads
Nombre de reads ok (= la moitié) et les séquences ne sont pas identiques pour le premier read (= on n'a pas 2x la même chose)
 echo $(zcat 63003856_chr22_1.fq.gz | wc -l)/4 | bc
1296055
 echo $(zcat 63003856_chr22_2.fq.gz | wc -l)/4 | bc
1296055
 [4]
 bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef 63003856_chr22_1.fq.gz 63003856_chr22_2.fq.gz  -o wtf.bam
 [M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1752492 sequences (240000014 bp)...
[M::mem_pestat]

[3.109094]

[10.19463]

SED: [2023-05-29 Mon 15:36]
****** DONE 1 SNV  : ok !
CLOSED: [2023-05-20 Sat 19:35] SCHEDULED: <2023-05-20 Sat>
#+begin_src
 make run READS="tests/bamscissors/corrected_{1,2}.fq.gz"
Puis on lance le pipeline sur correct_1
- [X] Variant visible dans IGV
- [X] Variant visible après alignement
- [X] Variant visible après appel de variant
****** KILL Tester SNV chromosome 22
CLOSED: [2023-05-29 Mon 15:36] SCHEDULED: <2023-05-20 Sat>
***** KILL PHase 2 : chr22, VAF variable
CLOSED: [2023-06-12 Mon 23:27] SCHEDULED: <2023-06-03 Sat>
****** DONE de nombreux reads sont perdus -> ok sur un SNV en alignant sur chromosome 22
CLOSED: [2023-05-29 Mon 15:38]
Problème dansr le BAM car sans les insertion
******* DONE Filtrer les reads sans pair : idem
CLOSED: [2023-05-23 Tue 00:01]
FOUND:Found 16662 unpaired mates
	at htsjdk.samtools.SAMUtils.processValidationError(SAMUtils.java:470)
	at picard.sam.SamToFastq.doWork(SamToFastq.java:224)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
ex: chr22:42213078
On essaie
samtools view ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135.bam NC_000022.11  -hf 0x2 -o 63003856_chr22.bam
Ne rale pas...
SCHEDULED: <2023-05-22 Mon>
******* DONE Problème de la conversion BAM -> fastq ?
CLOSED: [2023-05-24 Wed 23:19]
******** DONE Test bamtofastq sur le BAM originel: idem
CLOSED: [2023-05-23 Tue 01:16]
Dans ~/recherche/code/bisonex/Bamscissors.jl
samtools view ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135.bam NC_000022.11  -hf 0x2 -o 63003856_chr22.bam
On trie bien par nom de read
samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorted.bam
Conversion en fastq. Attention à bien prendre le *fichier trié* !
samtools bam2fq  -1 63003856_chr22_init1.fq.gz -2 63003856_chr22_init2.fq.gz  -n 63003856_chr22_sorted.bam
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 2592110 reads
On envoie sur le mésocentre
scp 63003856_chr22_init{1,2}.fq.gz meso:/Work/Users/apraga/bisonex/tests/bamscissors
On démarre un job avec 24 coeurs pour aller vite
srun -c 24 -p smp -t 1:00:00 --pty bash
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef 63003856_chr22_init1.fq.gz 63003856_chr22_init2.fq.gz | samtools sort -@24 -o output.bam -
Dans /home/alex/recherche/bisonex/code/BamScissors.jl/aligned
❯ scp meso:/Work/Users/apraga/bisonex/tests/bamscissors/output.bam*
******** DONE Avec samtools fastq
CLOSED: [2023-05-23 Tue 01:16]
samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorted.bam
samtools fastq 63003856_chr22_1.fq.gz -2 63003856_chr22_2.fq.gz -0 /dev/null -s /dev/null -o 63003856_chr22_sorted.bam
scp 63003856_chr22_{1,2}.fq.gz  meso:/Work/Users/apraga/bisonex/tests/bamscissors/
mesocentre
 bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef 63003856_chr22_1.fq.gz 63003856_chr22_2.fq.gz | samtools sort -@24 -o output.bam
 scp meso:/Work/Users/apraga/bisonex/tests/bamscissors/output.bam\* aligned/
******** DONE En rajoutant .fna dans le doserrie (+samtools fastq): idem
CLOSED: [2023-05-23 Tue 01:16]
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef* .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef* .
bwa mem -t 24 genomeRef 63003856_chr22_1.fq.gz 63003856_chr22_2.fq.gz | samtools sort -@24 -o output.bam
******** DONE Test picard : idem
CLOSED: [2023-05-23 Tue 01:16]
Dans bisonex/code/BamScissors.jl
❯ picard SamToFastq -I 63003856_chr22_sorted.bam -F testpicard1.fastq -F2 testpicard2.fastq
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef testpicard1.fastq.gz testpicard2.fastq.gz | samtools sort -@24 -o testpicard.bam -
******** DONE Il ne manque pas des reads dans les fastq :
CLOSED: [2023-05-23 Tue 01:26]
bisonex/code/BamScissors.jl on  bamscissors [!?] via ஃ v1.9.0
❯ samtools  flagstat aligned/output.bam
1306273 + 0 in total (QC-passed reads + QC-failed reads)
1296055 + 0 primary
0 + 0 secondary
10218 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
1304871 + 0 mapped (99.89% : N/A)
1294653 + 0 primary mapped (99.89% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
bisonex/code/BamScissors.jl on  bamscissors [!?] via ஃ v1.9.0
❯ samtools flagstat 63003856_chr22.bam
2609214 + 0 in total (QC-passed reads + QC-failed reads)
2592110 + 0 primary
0 + 0 secondary
17104 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
2609214 + 0 mapped (100.00% : N/A)
2592110 + 0 primary mapped (100.00% : N/A)
2592110 + 0 paired in sequencing
1296055 + 0 read1
1296055 + 0 read2
2592110 + 0 properly paired (100.00% : N/A)
2592110 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
❯ echo $(zcat 63003856_chr22_init2.fq.gz | wc -l)/4 | bc
1296055
bisonex/code/BamScissors.jl on  bamscissors [!?] via ஃ v1.9.0 took 2s
❯ echo $(zcat 63003856_chr22_init1.fq.gz | wc -l)/4 | bc
1296055
❯ samtools  flagstat 63003856_chr22_sorted.bam
2609214 + 0 in total (QC-passed reads + QC-failed reads)
2592110 + 0 primary
0 + 0 secondary
17104 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
2609214 + 0 mapped (100.00% : N/A)
2592110 + 0 primary mapped (100.00% : N/A)
2592110 + 0 paired in sequencing
1296055 + 0 read1
1296055 + 0 read2
2592110 + 0 properly paired (100.00% : N/A)
2592110 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
******** DONE Avec sort -O BAM idem
CLOSED: [2023-05-23 Tue 01:21]
******** DONE Singleton ou non mapped ? nonVirtPosition
CLOSED: [2023-05-23 Tue 01:22]
❯ samtools bam2fq  -1 63003856_chr22_init1.fq.gz -2 63003856_chr22_init2.fq.gz -0 both -s single.fq.gz  -n 63003856_chr22_sorted.bam
bisonex/code/BamScissors.jl on  bamscissors [!?] via ஃ v1.9.0
❯ wc -l 63003856_chr22_init* both single.fq.gz
   403540 63003856_chr22_init1.fq.gz
   404788 63003856_chr22_init2.fq.gz
        0 both
        0 single.fq.gz
   808328 total
******** Problème d'aligner car les reads sont bien dans le .fastq ?
Ex:
 zgrep "A00853:477:HMLWYDSX3:2:2624:2826:18630" 63003856_chr22_{1,2}.fq.gz
63003856_chr22_1.fq.gz:@A00853:477:HMLWYDSX3:2:2624:2826:18630
63003856_chr22_2.fq.gz:@A00853:477:HMLWYDSX3:2:2624:2826:18630
******* DONE Refaire la manip sur bam chr22 non modifié + mail Alexis
CLOSED: [2023-05-23 Tue 23:27]
[1]_samtools view ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135.bam NC_000022.11  -f 0x2 -o 63003856_chr22.bam
 Les reads sont bien tous mappé
samtools flagstat 63003856_chr22.bam
2609214 + 0 in total (QC-passed reads + QC-failed reads)
2592110 + 0 primary
0 + 0 secondary
17104 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
2609214 + 0 mapped (100.00% : N/A)
[2] samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorted.bam
flagstat idem
[3] samtools fastq -1 63003856_chr22_1.fq.gz -2 63003856_chr22_2.fq.gz -0 /dev/null -s /dev/null -n 63003856_chr22_sorted.bam
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 2592110 reads
Nombre de reads ok (= la moitié) et les séquences ne sont pas identiques pour le premier read (= on n'a pas 2x la même chose)
 echo $(zcat 63003856_chr22_1.fq.gz | wc -l)/4 | bc
1296055
 echo $(zcat 63003856_chr22_2.fq.gz | wc -l)/4 | bc
1296055
 [4]
 bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef 63003856_chr22_1.fq.gz 63003856_chr22_2.fq.gz  -o wtf.bam
 [M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 1752492 sequences (240000014 bp)...
[M::mem_pestat]

Replacement in projects/bisonex.org at line 49 [5.35]

B:BD[11.786] → [11.786:5728]

B:BD[11.5728] → [3.114037:128403]

CCBDCBDCCCFBD;EEBEBBABCEC:EEBEAADCFCDFBFECCFCFFFFCCGFEDGFBBEEDCAECCEEBCECBDBCEEDCCBCBFAECCFEACAEAEBCCDCBCBFB:;CAEDCAEDBEEEEDC?<ECFBCDBCCCEDAA
#+begin_src
zgrep -A 3 "A00853:477:HMLWYDSX3:1:1413:4390:28573" /Work/Projects/bisonex/centogene/fastq/2200467051_63003856/63003856_S135_R1_001.fastq.gz
#+end_src
#+RESULTS:
: @A00853:477:HMLWYDSX3:1:1413:4390:28573 1:N:0:ATTCCACACA+TAGGCGATTG
AGGGTTACCACCACCACCCTGACAGGAGATATTCTAGGAGTACTCAAGAGCATCAGGGGATGGCTGGTAGCCTAGAAGGAACCACAAGGCCCAATGTCTTGGTTAGTCAAACCAATGAATTAGCTAGCAGGGGCCTTCTGAACAAAAGCAT
: +
: FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFF
******** DONE Regarder la qualité après bwa mem vs applybqsr: différente
CLOSED: [2023-05-24 Wed 22:18]
Sur le mésocentre, dans /Work/Users/apraga/bisonex/out/63003856_S135_R/preprocessing
$ samtools view mapped/63003856_S135_R.bam NC_000022.11 | rg "A00853:477:HMLWYDSX3:1:1413:4390:28573"
A00853:477:HMLWYDSX3:1:1413:4390:28573	163	NC_000022.11	42212845	0	151M	=	42212883	189	CCCAGGGGCCCCAGTGGGGATTTTCTAATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT	FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:151	MC:Z:151M	AS:i:151	XS:i:151	RG:Z:sample
A00853:477:HMLWYDSX3:1:1413:4390:28573	83	NC_000022.11	42212883	0	151M	=	42212845	-189	ATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACTCCTAGAATATCTCCTGTCAGGGTGGTGGTGGTAACCCT	FFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:151	MC:Z:151M	AS:i:151	XS:i:151	RG:Z:sample
samtools view applybqsr/63003856_S135_R.bam NC_000022.11 | rg "A00853:477:HMLWYDSX3:1:1413:4390:28573"
A00853:477:HMLWYDSX3:1:1413:4390:28573	163	NC_000022.11	42212845	0	151M	=	42212883	189	CCCAGGGGCCCCAGTGGGGATTTTCTAATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT	ACC+FBCDCBBBAEAEDEEBBCCCECACBAEBEBDCCBCBFDCCCCFACEBEBCEEDCCCCFDCAEDCACBCEBBCFEACCFBDCACDCBCEBDBBCFEEDCCCFAFEACECCCECAEEDCADCBEDC7BEBCCCFBAFDCECCFBEAACA	MC:Z:151M	MD:Z:151	PG:Z:MarkDuplicates	RG:Z:sample	NM:i:0	AS:i:151	XS:i:151
A00853:477:HMLWYDSX3:1:1413:4390:28573	83	NC_000022.11	42212883	0	151M	=	42212845	-189	ATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACTCCTAGAATATCTCCTGTCAGGGTGGTGGTGGTAACCCT	AADECCCBDCBFCE<?CDEEEEBDEACDEAC;:BFBCBCDCCBEAEACAEFCCEAFBCBCCDEECBDBCECBEECCEACDEEBBFGDEFGCCFFFFCFCCEFBFDCFCDAAEBEE:CECBABBEBEE;DBFCCCDBCDBCCBBC?@BEEDA	MC:Z:151M	MD:Z:151	PG:Z:MarkDuplicates	RG:Z:sample	NM:i:0	AS:i:151	XS:i:151
******** DONE Réaligner à partir de la sortie de bwa mem
CLOSED: [2023-05-24 Wed 22:32]
#+begin_src sh
cd out/63003856_S135_R/preprocessing/mapped/
samtools view 63003856_S135_R.bam NC_000022.11  -f 0x2 -o 63003856_chr22.bam
samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorted.bam
samtools fastq -1 63003856_chr22_1.fq.gz -2 63003856_chr22_2.fq.gz -0 /dev/null -s /dev/null -n 63003856_chr22_sorted.bam
#+end_src
ON vérifie la qualité
#+begin_src
zgrep -A 3 "A00853:477:HMLWYDSX3:1:1413:4390:28573" 63003856_chr22_1.fq.gz
#+end_src
#+RESULTS:
: @A00853:477:HMLWYDSX3:1:1413:4390:28573
: AGGGTTACCACCACCACCCTGACAGGAGATATTCTAGGAGTACTCAAGAGCATCAGGGGATGGCTGGTAGCCTAGAAGGAACCACAAGGCCCAATGTCTTGGTTAGTCAAACCAATGAATTAGCTAGCAGGGGCCTTCTGAACAAAAGCAT
: +
: FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFF
#+begin_src
NXF_OPTS=-D"user.name=apraga" nextflow run main.nf -c nextflow.config  -profile standard,helios -resume  --input="out/63003856_S135_R/preprocessing/mapped/63003856_chr22_{1,2}.fq.gz" --outdir=out/63003856_chr22-from-mapped
#+end_src
Puis ::
#+begin_src
cd /Work/Users/apraga/bisonex/out/63003856_chr22-from-mapped/63003856_chr22/preprocessing/mapped
samtools view 63003856_chr22.bam | rg "A00853:477:HMLWYDSX3:1:1413:4390:28573"
#+end_src
#+RESULTS:
: A00853:477:HMLWYDSX3:1:1413:4390:28573	163	NW_014040930.1	115017	0	151M	=	115055	189	CCCAGGGGCCCCAGTGGGGATTTTCTAATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT	FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:151	MC:Z:151M	AS:i:151	XS:i:151	RG:Z:sample
: A00853:477:HMLWYDSX3:1:1413:4390:28573	83	NW_014040930.1	115055	0	151M	=	115017	-189	ATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGA
CATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACTCCTAGAATATCTCCTGTCAGGGTGGTGGTGGTAACCCT	FFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:151	MC:Z:151M	AS:i:151	XS:i:151	RG:Z:sample
******* DONE Aligner sur génome de référence limité au chromosome 22
CLOSED: [2023-05-24 Wed 23:18]
******** KILL Test données non modifiées
CLOSED: [2023-05-24 Wed 23:18]
/Work/Users/apraga/bisonex/tests/bamscissors
#+begin_src
cd /Work/Groups/bisonex/data/genome/GRCh38.p13/
mkdir chr22/
samtools faidx genomeRef.fna NC_000022.11 > chr22/chr22.fna
cd chr22
samtools faidx chr22.fna
bwa index chr22.fna
#+end_src
#+begin_src
cd /Work/Users/apraga/bisonex/tests/bamscissors
ln -s ../../out/63003856_S135_R/preprocessing/applybqsr/63003856_chr22_{1,2}.fq.gz .
srun -c 24 -p smp -t 1:00:00 --pty bash
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/chr22/chr22.fna 63003856_chr22_1.fq.gz 63003856_chr22_1.fq.gz -o smallref.sam
#+end_src
******** DONE Test données modifiées: ok
CLOSED: [2023-05-24 Wed 23:18]
Données dans data/init
#+begin_src sh
time julia insertVariant.jl
rsync -avz data/init/*.fq.gz meso:/Work/Users/apraga/bisonex/tests/bamscissors/
#+end_src
#+begin_src
srun -c 24 -p smp -t 1:00:00 --pty bash
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/chr22/chr22.fna 63003856_chr22_1.fq.gz 63003856_chr22_1.fq.gz | samtools sort -@24 - -o smallref.bam
#+end_src
#+begin_src
rsync -avz meso:/Work/Users/apraga/bisonex/tests/bamscissors/smallref.bam mapped/
#+end_src
****** DONE Test haplotypecaller 1 variant
CLOSED: [2023-05-29 Mon 15:38]
****** DONE Test haplotypecaller tous les variants
****** DONE Comprendre pourquoi la répartiton ne suit pas la loi normale
CLOSED: [2023-06-01 Thu 21:44]
Certains hétérozygote soint à 0.01 ou 1...
******* DONE augmenter le nombre d'échantillions: idem
CLOSED: [2023-05-31 Wed 22:24]
******* DONE Vérifier le nombre de reads marqué vs édité
CLOSED: [2023-06-01 Thu 21:44]
******* DONE vérifier que 100 appel à rand(d, 1)[1] est semblable à un appel de rand(d, 100)
CLOSED: [2023-05-31 Wed 22:24]
julia> df = vcat(DataFrame(:y => z, :type => "z"), DataFrame(:y => y, :type => "y"));
julia> y = [rand(d, 1)[1] for x in 1:1000];
julia> z = rand(d,1000);
julia> df = vcat(DataFrame(:y => z, :type => "z"), DataFrame(:y => y, :type => "y"));
 draw(data(df)*histogram(bins=100)*mapping(:y, color=:type,dodge=:type))
****** DONE Améliorer les performances
CLOSED: [2023-06-02 Fri 23:39]
#+begin_src julia
@time include("xamscissors.jl")
#+end_src
430s pour chromosome 22. Majorité dans l'édition de reads:
******* DONE Inserér tous les variants d'un reads d'un coup
CLOSED: [2023-06-01 Thu 23:09]
Ne change rien
******* DONE Test avec -t4: idem
CLOSED: [2023-06-01 Thu 23:17]
******* DONE Test mésocentre : idem
CLOSED: [2023-06-01 Thu 23:40]
348s
******* Changer la structure de données des
Dataframe -> dict = les performances horribles ont disparuse
****** TODO Refaire le test avec la nouvelle version
******* DONE Génération des données
CLOSED: [2023-06-02 Fri 23:40]
Mésocentre
#+begin_src sh
cd /Work/Users/apraga/bisonex/out/63003856_S135_R/preprocessing/mapped
samtools view 63003856_S135_R.bam NC_000022.11 -o 63003856_S135_R_chr22.bam
samtools index 63003856_S135_R_chr22.bam
cp 63003856_S135_R_chr22.bam* /Work/Users/apraga/bisonex/tests/xamscissors/
cd /Work/Users/apraga/bisonex/tests/xamscissors
#+end_src
On génère les données
#+begin_src julia
using XAMScissors
insertSNV("./63003856_S135_R_chr22.bam", "snvs_chr22.csv", "out")
#+end_src
Puis
#+begin_src sh
julia xamscissors.jl
#+end_src
******* DONE Run
CLOSED: [2023-06-03 Sat 18:26]
NXF_OPTS=-D"user.name=${USER}" nextflow run workflows/runInserted.nf -profile standard,helios  --input="tests/xamscissors/out/inserted_{1,2}.fq.gz"
******* DONE Après haplotypecaller : ok
CLOSED: [2023-06-03 Sat 18:27] SCHEDULED: <2023-06-03 Sat>
******* TODO Après filtre vep
SCHEDULED: <2023-06-03 Sat>
***** TODO PHase 3 : tous les SNV
SCHEDULED: <2023-06-03 Sat>
****** DONE Générer les données
CLOSED: [2023-06-03 Sat 20:16] SCHEDULED: <2023-06-03 Sat>
#+begin_src julia
using XAMScissors
insertSNV("../../out/63003856_S135_R/preprocessing/mapped/63003856_S135_R.bam", "snvs.csv", "out")
#+end_src
temps d'exécution 73min
#+begin_src sh
nohup bash -c 'time julia xamscissors.jl' &
xamscissors-63003856/*.fq.gz /Work/Groups/bisonex/data/xamscissors/
#+end_src
****** DONE Regénérer avec @time pour avoir les performaces
CLOSED: [2023-06-03 Sat 21:45]
markReads 6.265202 seconds (1.36 M allocations: 137.090 MiB, 1.00% gc time, 9.79% compilation time)
editReads 1327.701623 seconds (1.03 G allocations: 81.996 GiB, 0.59% gc time, 0.03% compilation time)
samtools index 117.743727 seconds (53 allocations: 1.883 KiB)
samtools sort 2820.074930 seconds (66 allocations: 2.789 KiB)
bam2fastq 134.148952 seconds (794 allocations: 40.539 KiB, 0.01% compilation time)
real	73m33.273s
user	77m38.194s
sys	1m26.684s
[bam_sort_core] merging from 60 files and 1 in-memory blocks...
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 126905130 reads
real	73m6.934s
user	77m25.397s
sys	1m21.339s
****** TODO Après haplotypecaller 556/590, majorité = échec alignement
SCHEDULED: <2023-06-04 Sun>
Haplotypecaller 556 found over 590
Amongst 34 missed variant, 2 have a mapping quality > 0
2×7 DataFrame
 Row │ chrom         pos        ref      alt      zygosity  meanQual   stdQual
     │ String15      Int64      String1  String1  String7   Float64    Float64
─────┼─────────────────────────────────────────────────────────────────────────
   1 │ NC_000017.11   39672244  G        A        het       60.0       0.0
   2 │ NC_000001.11  155235252  A        G        het        0.258065  2.48868
NC_000017.11   39672244  G        A        het => ok, problème de représentation car 2 variant côte à cote
NC_000001.11  155235252  A        G        het => peu de reads alternatifs (9/93 donc ok)
Position: chromoe 1 et 6 surtout
34×7 DataFrame
 Row │ chrom         pos        ref      alt      zygosity
     │ String15      Int64      String1  String1  String7
─────┼──────────────────────────────────────────────────────
   1 │ NC_000001.11  153817496  A        T        het
   2 │ NC_000001.11  155235252  A        G        het
   3 │ NC_000001.11  155236268  G        A        het
   4 │ NC_000001.11  155290591  C        T        het
   5 │ NC_000001.11  155291918  G        A        het
   6 │ NC_000001.11  155294358  G        T        het
   7 │ NC_000002.12  149010343  C        T        het
   8 │ NC_000006.12   32039426  T        A        het
   9 │ NC_000006.12   32040110  G        T        het
  10 │ NC_000006.12   32040723  G        A        het
  11 │ NC_000006.12   32041006  C        T        het
  12 │ NC_000006.12   32041147  G        A        het
  13 │ NC_000006.12   33443054  G        T        het
  14 │ NC_000006.12   33451815  C        T        het
  15 │ NC_000006.12  170283230  C        A        het
  16 │ NC_000006.12  170283754  G        A        het
  17 │ NC_000006.12  170285637  T        C        het
  18 │ NC_000006.12  170289678  A        C        het
  19 │ NC_000010.11   87961118  G        A        het
  20 │ NC_000012.12    2449086  C        G        het
  21 │ NC_000015.10   74343027  C        T        het
  22 │ NC_000016.10   16163078  G        A        het
  23 │ NC_000016.10   21262032  C        G        het
  24 │ NC_000016.10     21962506  C        T        homo
  25 │ NC_000017.11    7513122  C        T        het
  26 │ NC_000017.11    7513752  C        T        het
  27 │ NC_000017.11   39672244  G        A        het
  28 │ NC_000017.11   46018710  C        T        het
  29 │ NC_000019.10   54144058  G        A        het
  30 │ NC_000021.9    43063074  A        G        het
  31 │ NC_000021.9    43426167  C        T        het
  32 │ NC_000022.11   18918421  A        G        het
  33 │ NC_000022.11   42087168  T        A        homo
  34 │ NC_000022.11   42213078  T        G        het
****** DONE Voir où est l'alignement alternatif: sur NW_ (zone supprimée)
CLOSED: [2023-06-04 Sun 22:15] SCHEDULED: <2023-06-04 Sun>
ex chr15 74343027
  A00853:477:HMLWYDSX3:2:2444:22354:28870
#+begin_src
cd /Work/Groups/bisonex/data/xamscissors
zgrep -A4 "A00853:477:HMLWYDSX3:2:2444:22354:28870" *.fq.gz
 #+end_src
63003856_xamscissors_1.fq.gz:@A00853:477:HMLWYDSX3:2:2444:22354:28870
63003856_xamscissors_1.fq.gz:CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTTGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC
63003856_xamscissors_1.fq.gz:+
63003856_xamscissors_1.fq.gz:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFF,FFFFFF,FFFFFFFFFFFF:FF::FF
63003856_xamscissors_2.fq.gz:@A00853:477:HMLWYDSX3:2:2444:22354:28870
63003856_xamscissors_2.fq.gz:GACAGAAAGGAAGTGTTCACCACGATTACCGTGGCATCCTCTACAGACTCCTGGGAGACAGCAAGATGTCCTTCGAGGACATCAAGGCCAACGTCACAGAGATGCCGGCAGGAGGGGTGGACACGGTG
63003856_xamscissors_2.fq.gz:+
63003856_xamscissors_2.fq.gz:FF:FFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:F:FF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,:FFF,FFFFFF:FFFFFFFFFFFFF
******* DONE Avec BLAT: sur _fix
CLOSED: [2023-06-04 Sun 21:07]
1er =
   ACTIONS      QUERY   SCORE START   END QSIZE IDENTITY  CHROM                 STRAND  START       END   SPAN
--------------------------------------------------------------------------------------------------------------
browser details YourSeq   124     1   128   128    98.5%  chr15_ML143370v1_fix  +      172243    172370    128   What is chrom_fix?
browser details YourSeq   124     1   128   128    98.5%  chr15                 +    74342974  74343101    128
browser details YourSeq    23     1    25   128    96.0%  chr19                 -    33396097  33396121     25
Second
--------------------------------------------------------------------------------------------------------------
browser details YourSeq   126     1   128   128    99.3%  chr15_ML143370v1_fix  -      172243    172370    128   What is chrom_fix?
browser details YourSeq   126     1   128   128    99.3%  chr15                 -    74342974  74343101    128
browser details YourSeq    23   104   128   128    96.0%  chr19                 +    33396097  33396121     25
******* DONE Bwa mem à la main GRCh38.p13 : on est dans une zone NW
CLOSED: [2023-06-04 Sun 21:51]
On met les 2 reads dans des fichiers séparés puis
#+begin_src sh
cd /Work/Users/apraga/bisonex/tests/xamscissors/align
bwa mem /Work/Groups/bisonex/data/genome/GRCh38.p13/bwa/genomeRef test1.fq test2.fq
#+end_src
A00853:477:HMLWYDSX3:2:2444:22354:28870	97	NW_021160016.1	172243	0	128M	=	172243	128	CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTTGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFF,FFFFFF,FFFFFFFFFFFF:FF::FF	NM:i:2	MD:Z:22A30C7MC:Z:128M	AS:i:118	XS:i:118	XA:Z:NC_000015.10,+74342974,128M,2;
A00853:477:HMLWYDSX3:2:2444:22354:28870	145	NW_021160016.1	172243	0	128M	=	172243	-128	CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTCGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC	FFFFFFFFFFFFF:FFFFFF,FFF:,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFF:FF	NM:i:1	MD:Z:22A105	MC:Z:128M	AS:i:123	XS:i:123	XA:Z:NC_000015.10,-74342974,128M,1;
******* DONE GRCh38.p14: idem
CLOSED: [2023-06-04 Sun 21:51]
A00853:477:HMLWYDSX3:2:2444:22354:28870	97	NW_021160016.1	172243	0	128M	=	172243	128	CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTTGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFF,FFFFFF,FFFFFFFFFFFF:FF::FF	NM:i:2	MD:Z:22A30C7MC:Z:128M	AS:i:118	XS:i:118	XA:Z:NC_000015.10,+74342974,128M,2;
A00853:477:HMLWYDSX3:2:2444:22354:28870	145	NW_021160016.1	172243	0	128M	=	172243	-128	CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTCGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC	FFFFFFFFFFFFF:FFFFFF,FFF:,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFF:FF	NM:i:1	MD:Z:22A105	MC:Z:128M	AS:i:123	XS:i:123	XA:Z:NC_000015.10,-74342974,128M,1;
******* DONE GRCh38 : ok
CLOSED: [2023-06-04 Sun 22:15]
 bwa mem /Work/Projects/bisonex/data/genome/GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna test1.fq test2.fq
****** DONE Vérifier que les reads ont la même qualité sur les fichiers d'origine: oui
CLOSED: [2023-06-04 Sun 21:07]
****** DONE Supprimer les NW_ ?
CLOSED: [2023-06-10 Sat 10:40] SCHEDULED: <2023-06-04 Sun>
@A00853:477:HMLWYDSX3:3:2114:14742:8860
CAGGCCAGCCGCTCAGCCCGCTCCTTTCACCCTCTGCAGGAGAGCCTCGTGGCAGGCCAGTGGAGGGACATGATGGACTACATGCTCCAAGGGGTGGCGCAGCCGAGCATGGAAGAGGGCTCTGGACAGCTCCTGGAAGGGCACTTGCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@A00853:477:HMLWYDSX3:3:2114:14742:8860
CTTTTGCTTGTCCCCAGGACGCACCTCAGGGTGGTGAAGCAAAAAAACCACGGCCCAGGAGAGGGTGGGTGCTGTGGTCTCAGTGCCACCGATCAGGAGGTCCACTGCAGCCATGTGCAAGTGCCCTTCCAGGAGCTGTCCAGAGCCCTCT
+
FFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFF,FFFFFFFFFFFF:F:FFFF:FFFFF,,FFF:FFFFFFFFFF,FFFFFFF,FFFFFFFFFFF,FFFFFFFFF:FFFF,F:FFFFF:FFFFFFFFF:FFFF,FFFFFFFFF
****** TODO Supprimer NW_ et NT_
**** TODO Test Indel
*** Divers
**** DONE Vérifier nombre de reads fastq - bam
CLOSED: [2022-10-09 Sun 22:31]

[11.786]

CCBDCBDCCCFBD;EEBEBBABCEC:EEBEAADCFCDFBFECCFCFFFFCCGFEDGFBBEEDCAECCEEBCECBDBCEEDCCBCBFAECCFEACAEAEBCCDCBCBFB:;CAEDCAEDBEEEEDC?<ECFBCDBCCCEDAA
#+begin_src
zgrep -A 3 "A00853:477:HMLWYDSX3:1:1413:4390:28573" /Work/Projects/bisonex/centogene/fastq/2200467051_63003856/63003856_S135_R1_001.fastq.gz
#+end_src
#+RESULTS:
: @A00853:477:HMLWYDSX3:1:1413:4390:28573 1:N:0:ATTCCACACA+TAGGCGATTG
AGGGTTACCACCACCACCCTGACAGGAGATATTCTAGGAGTACTCAAGAGCATCAGGGGATGGCTGGTAGCCTAGAAGGAACCACAAGGCCCAATGTCTTGGTTAGTCAAACCAATGAATTAGCTAGCAGGGGCCTTCTGAACAAAAGCAT
: +
: FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFF
******** DONE Regarder la qualité après bwa mem vs applybqsr: différente
CLOSED: [2023-05-24 Wed 22:18]
Sur le mésocentre, dans /Work/Users/apraga/bisonex/out/63003856_S135_R/preprocessing
$ samtools view mapped/63003856_S135_R.bam NC_000022.11 | rg "A00853:477:HMLWYDSX3:1:1413:4390:28573"
A00853:477:HMLWYDSX3:1:1413:4390:28573	163	NC_000022.11	42212845	0	151M	=	42212883	189	CCCAGGGGCCCCAGTGGGGATTTTCTAATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT	FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:151	MC:Z:151M	AS:i:151	XS:i:151	RG:Z:sample
A00853:477:HMLWYDSX3:1:1413:4390:28573	83	NC_000022.11	42212883	0	151M	=	42212845	-189	ATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACTCCTAGAATATCTCCTGTCAGGGTGGTGGTGGTAACCCT	FFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:151	MC:Z:151M	AS:i:151	XS:i:151	RG:Z:sample
samtools view applybqsr/63003856_S135_R.bam NC_000022.11 | rg "A00853:477:HMLWYDSX3:1:1413:4390:28573"
A00853:477:HMLWYDSX3:1:1413:4390:28573	163	NC_000022.11	42212845	0	151M	=	42212883	189	CCCAGGGGCCCCAGTGGGGATTTTCTAATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT	ACC+FBCDCBBBAEAEDEEBBCCCECACBAEBEBDCCBCBFDCCCCFACEBEBCEEDCCCCFDCAEDCACBCEBBCFEACCFBDCACDCBCEBDBBCFEEDCCCFAFEACECCCECAEEDCADCBEDC7BEBCCCFBAFDCECCFBEAACA	MC:Z:151M	MD:Z:151	PG:Z:MarkDuplicates	RG:Z:sample	NM:i:0	AS:i:151	XS:i:151
A00853:477:HMLWYDSX3:1:1413:4390:28573	83	NC_000022.11	42212883	0	151M	=	42212845	-189	ATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACTCCTAGAATATCTCCTGTCAGGGTGGTGGTGGTAACCCT	AADECCCBDCBFCE<?CDEEEEBDEACDEAC;:BFBCBCDCCBEAEACAEFCCEAFBCBCCDEECBDBCECBEECCEACDEEBBFGDEFGCCFFFFCFCCEFBFDCFCDAAEBEE:CECBABBEBEE;DBFCCCDBCDBCCBBC?@BEEDA	MC:Z:151M	MD:Z:151	PG:Z:MarkDuplicates	RG:Z:sample	NM:i:0	AS:i:151	XS:i:151
******** DONE Réaligner à partir de la sortie de bwa mem
CLOSED: [2023-05-24 Wed 22:32]
#+begin_src sh
cd out/63003856_S135_R/preprocessing/mapped/
samtools view 63003856_S135_R.bam NC_000022.11  -f 0x2 -o 63003856_chr22.bam
samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorted.bam
samtools fastq -1 63003856_chr22_1.fq.gz -2 63003856_chr22_2.fq.gz -0 /dev/null -s /dev/null -n 63003856_chr22_sorted.bam
#+end_src
ON vérifie la qualité
#+begin_src
zgrep -A 3 "A00853:477:HMLWYDSX3:1:1413:4390:28573" 63003856_chr22_1.fq.gz
#+end_src
#+RESULTS:
: @A00853:477:HMLWYDSX3:1:1413:4390:28573
: AGGGTTACCACCACCACCCTGACAGGAGATATTCTAGGAGTACTCAAGAGCATCAGGGGATGGCTGGTAGCCTAGAAGGAACCACAAGGCCCAATGTCTTGGTTAGTCAAACCAATGAATTAGCTAGCAGGGGCCTTCTGAACAAAAGCAT
: +
: FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFF
#+begin_src
NXF_OPTS=-D"user.name=apraga" nextflow run main.nf -c nextflow.config  -profile standard,helios -resume  --input="out/63003856_S135_R/preprocessing/mapped/63003856_chr22_{1,2}.fq.gz" --outdir=out/63003856_chr22-from-mapped
#+end_src
Puis ::
#+begin_src
cd /Work/Users/apraga/bisonex/out/63003856_chr22-from-mapped/63003856_chr22/preprocessing/mapped
samtools view 63003856_chr22.bam | rg "A00853:477:HMLWYDSX3:1:1413:4390:28573"
#+end_src
#+RESULTS:
: A00853:477:HMLWYDSX3:1:1413:4390:28573	163	NW_014040930.1	115017	0	151M	=	115055	189	CCCAGGGGCCCCAGTGGGGATTTTCTAATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT	FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:151	MC:Z:151M	AS:i:151	XS:i:151	RG:Z:sample
: A00853:477:HMLWYDSX3:1:1413:4390:28573	83	NW_014040930.1	115055	0	151M	=	115017	-189	ATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACTCCTAGAATATCTCCTGTCAGGGTGGTGGTGGTAACCCT	FFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:151	MC:Z:151M	AS:i:151	XS:i:151	RG:Z:sample
******* DONE Aligner sur génome de référence limité au chromosome 22
CLOSED: [2023-05-24 Wed 23:18]
******** KILL Test données non modifiées
CLOSED: [2023-05-24 Wed 23:18]
/Work/Users/apraga/bisonex/tests/bamscissors
#+begin_src
cd /Work/Groups/bisonex/data/genome/GRCh38.p13/
mkdir chr22/
samtools faidx genomeRef.fna NC_000022.11 > chr22/chr22.fna
cd chr22
samtools faidx chr22.fna
bwa index chr22.fna
#+end_src
#+begin_src
cd /Work/Users/apraga/bisonex/tests/bamscissors
ln -s ../../out/63003856_S135_R/preprocessing/applybqsr/63003856_chr22_{1,2}.fq.gz .
srun -c 24 -p smp -t 1:00:00 --pty bash
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/chr22/chr22.fna 63003856_chr22_1.fq.gz 63003856_chr22_1.fq.gz -o smallref.sam
#+end_src
******** DONE Test données modifiées: ok
CLOSED: [2023-05-24 Wed 23:18]
Données dans data/init
#+begin_src sh
time julia insertVariant.jl
rsync -avz data/init/*.fq.gz meso:/Work/Users/apraga/bisonex/tests/bamscissors/
#+end_src
#+begin_src
srun -c 24 -p smp -t 1:00:00 --pty bash
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/chr22/chr22.fna 63003856_chr22_1.fq.gz 63003856_chr22_1.fq.gz | samtools sort -@24 - -o smallref.bam
#+end_src
#+begin_src
rsync -avz meso:/Work/Users/apraga/bisonex/tests/bamscissors/smallref.bam mapped/
#+end_src
****** DONE Test haplotypecaller 1 variant
CLOSED: [2023-05-29 Mon 15:38]
****** DONE Test haplotypecaller tous les variants
****** DONE Comprendre pourquoi la répartiton ne suit pas la loi normale
CLOSED: [2023-06-01 Thu 21:44]
Certains hétérozygote soint à 0.01 ou 1...
******* DONE augmenter le nombre d'échantillions: idem
CLOSED: [2023-05-31 Wed 22:24]
******* DONE Vérifier le nombre de reads marqué vs édité
CLOSED: [2023-06-01 Thu 21:44]
******* DONE vérifier que 100 appel à rand(d, 1)[1] est semblable à un appel de rand(d, 100)
CLOSED: [2023-05-31 Wed 22:24]
julia> df = vcat(DataFrame(:y => z, :type => "z"), DataFrame(:y => y, :type => "y"));
julia> y = [rand(d, 1)[1] for x in 1:1000];
julia> z = rand(d,1000);
julia> df = vcat(DataFrame(:y => z, :type => "z"), DataFrame(:y => y, :type => "y"));
 draw(data(df)*histogram(bins=100)*mapping(:y, color=:type,dodge=:type))
****** DONE Améliorer les performances
CLOSED: [2023-06-02 Fri 23:39]
#+begin_src julia
@time include("xamscissors.jl")
#+end_src
430s pour chromosome 22. Majorité dans l'édition de reads:
******* DONE Inserér tous les variants d'un reads d'un coup
CLOSED: [2023-06-01 Thu 23:09]
Ne change rien
******* DONE Test avec -t4: idem
CLOSED: [2023-06-01 Thu 23:17]
******* DONE Test mésocentre : idem
CLOSED: [2023-06-01 Thu 23:40]
348s
******* Changer la structure de données des
Dataframe -> dict = les performances horribles ont disparuse
****** KILL Refaire le test avec la nouvelle version
CLOSED: [2023-06-12 Mon 23:27]
******* DONE Génération des données
CLOSED: [2023-06-02 Fri 23:40]
Mésocentre
#+begin_src sh
cd /Work/Users/apraga/bisonex/out/63003856_S135_R/preprocessing/mapped
samtools view 63003856_S135_R.bam NC_000022.11 -o 63003856_S135_R_chr22.bam
samtools index 63003856_S135_R_chr22.bam
cp 63003856_S135_R_chr22.bam* /Work/Users/apraga/bisonex/tests/xamscissors/
cd /Work/Users/apraga/bisonex/tests/xamscissors
#+end_src
On génère les données
#+begin_src julia
using XAMScissors
insertSNV("./63003856_S135_R_chr22.bam", "snvs_chr22.csv", "out")
#+end_src
Puis
#+begin_src sh
julia xamscissors.jl
#+end_src
******* DONE Run
CLOSED: [2023-06-03 Sat 18:26]
NXF_OPTS=-D"user.name=${USER}" nextflow run workflows/runInserted.nf -profile standard,helios  --input="tests/xamscissors/out/inserted_{1,2}.fq.gz"
******* DONE Après haplotypecaller : ok
CLOSED: [2023-06-03 Sat 18:27] SCHEDULED: <2023-06-03 Sat>
******* KILL Après filtre vep
CLOSED: [2023-06-12 Mon 23:27] SCHEDULED: <2023-06-03 Sat>
***** KILL PHase 3 : tous les SNV
CLOSED: [2023-06-12 Mon 23:28] SCHEDULED: <2023-06-03 Sat>
****** DONE Générer les données
CLOSED: [2023-06-03 Sat 20:16] SCHEDULED: <2023-06-03 Sat>
#+begin_src julia
using XAMScissors
insertSNV("../../out/63003856_S135_R/preprocessing/mapped/63003856_S135_R.bam", "snvs.csv", "out")
#+end_src
temps d'exécution 73min
#+begin_src sh
nohup bash -c 'time julia xamscissors.jl' &
xamscissors-63003856/*.fq.gz /Work/Groups/bisonex/data/xamscissors/
#+end_src
****** DONE Regénérer avec @time pour avoir les performaces
CLOSED: [2023-06-03 Sat 21:45]
markReads 6.265202 seconds (1.36 M allocations: 137.090 MiB, 1.00% gc time, 9.79% compilation time)
editReads 1327.701623 seconds (1.03 G allocations: 81.996 GiB, 0.59% gc time, 0.03% compilation time)
samtools index 117.743727 seconds (53 allocations: 1.883 KiB)
samtools sort 2820.074930 seconds (66 allocations: 2.789 KiB)
bam2fastq 134.148952 seconds (794 allocations: 40.539 KiB, 0.01% compilation time)
real	73m33.273s
user	77m38.194s
sys	1m26.684s
[bam_sort_core] merging from 60 files and 1 in-memory blocks...
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 126905130 reads
real	73m6.934s
user	77m25.397s
sys	1m21.339s
****** KILL Après haplotypecaller 556/590, majorité = échec alignement
CLOSED: [2023-06-12 Mon 23:27] SCHEDULED: <2023-06-04 Sun>
Haplotypecaller 556 found over 590
Amongst 34 missed variant, 2 have a mapping quality > 0
2×7 DataFrame
 Row │ chrom         pos        ref      alt      zygosity  meanQual   stdQual
     │ String15      Int64      String1  String1  String7   Float64    Float64
─────┼─────────────────────────────────────────────────────────────────────────
   1 │ NC_000017.11   39672244  G        A        het       60.0       0.0
   2 │ NC_000001.11  155235252  A        G        het        0.258065  2.48868
NC_000017.11   39672244  G        A        het => ok, problème de représentation car 2 variant côte à cote
NC_000001.11  155235252  A        G        het => peu de reads alternatifs (9/93 donc ok)
Position: chromoe 1 et 6 surtout
34×7 DataFrame
 Row │ chrom         pos        ref      alt      zygosity
     │ String15      Int64      String1  String1  String7
─────┼──────────────────────────────────────────────────────
   1 │ NC_000001.11  153817496  A        T        het
   2 │ NC_000001.11  155235252  A        G        het
   3 │ NC_000001.11  155236268  G        A        het
   4 │ NC_000001.11  155290591  C        T        het
   5 │ NC_000001.11  155291918  G        A        het
   6 │ NC_000001.11  155294358  G        T        het
   7 │ NC_000002.12  149010343  C        T        het
   8 │ NC_000006.12   32039426  T        A        het
   9 │ NC_000006.12   32040110  G        T        het
  10 │ NC_000006.12   32040723  G        A        het
  11 │ NC_000006.12   32041006  C        T        het
  12 │ NC_000006.12   32041147  G        A        het
  13 │ NC_000006.12   33443054  G        T        het
  14 │ NC_000006.12   33451815  C        T        het
  15 │ NC_000006.12  170283230  C        A        het
  16 │ NC_000006.12  170283754  G        A        het
  17 │ NC_000006.12  170285637  T        C        het
  18 │ NC_000006.12  170289678  A        C        het
  19 │ NC_000010.11   87961118  G        A        het
  20 │ NC_000012.12    2449086  C        G        het
  21 │ NC_000015.10   74343027  C        T        het
  22 │ NC_000016.10   16163078  G        A        het
  23 │ NC_000016.10   21262032  C        G        het
  24 │ NC_000016.10     21962506  C        T        homo
  25 │ NC_000017.11    7513122  C        T        het
  26 │ NC_000017.11    7513752  C        T        het
  27 │ NC_000017.11   39672244  G        A        het
  28 │ NC_000017.11   46018710  C        T        het
  29 │ NC_000019.10   54144058  G        A        het
  30 │ NC_000021.9    43063074  A        G        het
  31 │ NC_000021.9    43426167  C        T        het
  32 │ NC_000022.11   18918421  A        G        het
  33 │ NC_000022.11   42087168  T        A        homo
  34 │ NC_000022.11   42213078  T        G        het
****** DONE Voir où est l'alignement alternatif: sur NW_ (zone supprimée)
CLOSED: [2023-06-04 Sun 22:15] SCHEDULED: <2023-06-04 Sun>
ex chr15 74343027
  A00853:477:HMLWYDSX3:2:2444:22354:28870
#+begin_src
cd /Work/Groups/bisonex/data/xamscissors
zgrep -A4 "A00853:477:HMLWYDSX3:2:2444:22354:28870" *.fq.gz
 #+end_src
63003856_xamscissors_1.fq.gz:@A00853:477:HMLWYDSX3:2:2444:22354:28870
63003856_xamscissors_1.fq.gz:CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTTGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC
63003856_xamscissors_1.fq.gz:+
63003856_xamscissors_1.fq.gz:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFF,FFFFFF,FFFFFFFFFFFF:FF::FF
63003856_xamscissors_2.fq.gz:@A00853:477:HMLWYDSX3:2:2444:22354:28870
63003856_xamscissors_2.fq.gz:GACAGAAAGGAAGTGTTCACCACGATTACCGTGGCATCCTCTACAGACTCCTGGGAGACAGCAAGATGTCCTTCGAGGACATCAAGGCCAACGTCACAGAGATGCCGGCAGGAGGGGTGGACACGGTG
63003856_xamscissors_2.fq.gz:+
63003856_xamscissors_2.fq.gz:FF:FFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:F:FF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,:FFF,FFFFFF:FFFFFFFFFFFFF
******* DONE Avec BLAT: sur _fix
CLOSED: [2023-06-04 Sun 21:07]
1er =
   ACTIONS      QUERY   SCORE START   END QSIZE IDENTITY  CHROM                 STRAND  START       END   SPAN
--------------------------------------------------------------------------------------------------------------
browser details YourSeq   124     1   128   128    98.5%  chr15_ML143370v1_fix  +      172243    172370    128   What is chrom_fix?
browser details YourSeq   124     1   128   128    98.5%  chr15                 +    74342974  74343101    128
browser details YourSeq    23     1    25   128    96.0%  chr19                 -    33396097  33396121     25
Second
--------------------------------------------------------------------------------------------------------------
browser details YourSeq   126     1   128   128    99.3%  chr15_ML143370v1_fix  -      172243    172370    128   What is chrom_fix?
browser details YourSeq   126     1   128   128    99.3%  chr15                 -    74342974  74343101    128
browser details YourSeq    23   104   128   128    96.0%  chr19                 +    33396097  33396121     25
******* DONE Bwa mem à la main GRCh38.p13 : on est dans une zone NW
CLOSED: [2023-06-04 Sun 21:51]
On met les 2 reads dans des fichiers séparés puis
#+begin_src sh
cd /Work/Users/apraga/bisonex/tests/xamscissors/align
bwa mem /Work/Groups/bisonex/data/genome/GRCh38.p13/bwa/genomeRef test1.fq test2.fq
#+end_src
A00853:477:HMLWYDSX3:2:2444:22354:28870	97	NW_021160016.1	172243	0	128M	=	172243	128	CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTTGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFF,FFFFFF,FFFFFFFFFFFF:FF::FF	NM:i:2	MD:Z:22A30C7MC:Z:128M	AS:i:118	XS:i:118	XA:Z:NC_000015.10,+74342974,128M,2;
A00853:477:HMLWYDSX3:2:2444:22354:28870	145	NW_021160016.1	172243	0	128M	=	172243	-128	CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTCGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC	FFFFFFFFFFFFF:FFFFFF,FFF:,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFF:FF	NM:i:1	MD:Z:22A105	MC:Z:128M	AS:i:123	XS:i:123	XA:Z:NC_000015.10,-74342974,128M,1;
******* DONE GRCh38.p14: idem
CLOSED: [2023-06-04 Sun 21:51]
A00853:477:HMLWYDSX3:2:2444:22354:28870	97	NW_021160016.1	172243	0	128M	=	172243	128	CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTTGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC	FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFF,FFFFFF,FFFFFFFFFFFF:FF::FF	NM:i:2	MD:Z:22A30C7MC:Z:128M	AS:i:118	XS:i:118	XA:Z:NC_000015.10,+74342974,128M,2;
A00853:477:HMLWYDSX3:2:2444:22354:28870	145	NW_021160016.1	172243	0	128M	=	172243	-128	CACCGTGTCCACCCCTCCTGCCGGCATCTCTGTGACGTTGGCCTTGATGTCCTCGAAGGACATCTTGCTGTCTCCCAGGAGTCTGTAGAGGATGCCACGGTAATCGTGGTGAACACTTCCTTTCTGTC	FFFFFFFFFFFFF:FFFFFF,FFF:,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFF:FF	NM:i:1	MD:Z:22A105	MC:Z:128M	AS:i:123	XS:i:123	XA:Z:NC_000015.10,-74342974,128M,1;
******* DONE GRCh38 : ok
CLOSED: [2023-06-04 Sun 22:15]
 bwa mem /Work/Projects/bisonex/data/genome/GRCh38/GCA_000001405.15_GRCh38_full_analysis_set.fna test1.fq test2.fq
****** DONE Vérifier que les reads ont la même qualité sur les fichiers d'origine: oui
CLOSED: [2023-06-04 Sun 21:07]
****** DONE Supprimer les NW_ ?
CLOSED: [2023-06-10 Sat 10:40] SCHEDULED: <2023-06-04 Sun>
@A00853:477:HMLWYDSX3:3:2114:14742:8860
CAGGCCAGCCGCTCAGCCCGCTCCTTTCACCCTCTGCAGGAGAGCCTCGTGGCAGGCCAGTGGAGGGACATGATGGACTACATGCTCCAAGGGGTGGCGCAGCCGAGCATGGAAGAGGGCTCTGGACAGCTCCTGGAAGGGCACTTGCAC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@A00853:477:HMLWYDSX3:3:2114:14742:8860
CTTTTGCTTGTCCCCAGGACGCACCTCAGGGTGGTGAAGCAAAAAAACCACGGCCCAGGAGAGGGTGGGTGCTGTGGTCTCAGTGCCACCGATCAGGAGGTCCACTGCAGCCATGTGCAAGTGCCCTTCCAGGAGCTGTCCAGAGCCCTCT
+
FFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFF,FFFFFFFFFFFF:F:FFFF:FFFFF,,FFF:FFFFFFFFFF,FFFFFFF,FFFFFFFFFFF,FFFFFFFFF:FFFF,F:FFFFF:FFFFFFFFF:FFFF,FFFFFFFFF
****** DONE Supprimer NW_ et NT_
***** TODO Phase 2 : chr22, vaf variable :TIT:
SCHEDULED: <2023-06-16 Fri>
CLOSED: [2023-06-12 Mon 23:27]
***** TODO Phase 3 : tous SNV, vaf variable :TIT:
SCHEDULED: <2023-06-16 Fri>
CLOSED: [2023-06-12 Mon 23:27]
**** TODO Test Indel
*** Divers
**** DONE Vérifier nombre de reads fastq - bam
CLOSED: [2022-10-09 Sun 22:31]