apraga/org - Change 3ZNNLNT7FVFHXCAVNFT4WYBVIBZHU4DPLRPDRJRRL65UE4ASJL7QC

Cleaning up lists and projects

Created by Alexis Praga on April 29, 2024

3ZNNLNT7FVFHXCAVNFT4WYBVIBZHU4DPLRPDRJRRL65UE4ASJL7QC

Dependencies

In channels

main

Change contents

File deletion: projects
BF:BFD[4.2] → [5.14:33]
BF:BFD[5.33] → [5.13:13]
File deletion: art-capture-1.png
BF:BFD[5.13] → [6.361879:361927]
BF:BFD[6.361927] → [6.320204:320204]
B:BD[6.320204] → [6.320205:361878]
File deletion: check-snv-chr15.png
BF:BFD[5.13] → [7.352764:352814]
BF:BFD[7.352814] → [7.295742:295742]
B:BD[7.295742] → [7.295743:352763]
File deletion: art-exon6-offset1000.png
BF:BFD[5.13] → [6.320147:320202]
BF:BFD[6.320202] → [6.230520:230520]
B:BD[6.230520] → [6.230521:320146]
File deletion: insertion-demo.png
BF:BFD[5.13] → [7.295688:295737]
BF:BFD[7.295737] → [7.250481:250481]
B:BD[7.250481] → [7.250482:295687]
File deletion: simuscop-success.png
BF:BFD[5.13] → [7.250424:250475]
BF:BFD[7.250475] → [7.177464:177464]
B:BD[7.177464] → [7.177465:250423]
File deletion: illumina-ref-exon6.png
BF:BFD[5.13] → [6.206377:206430]
BF:BFD[6.206430] → [6.139444:139444]
B:BD[6.139444] → [6.139445:206376]
File deletion: test-intersect-chr15.png
BF:BFD[5.13] → [7.177407:177462]
BF:BFD[7.177462] → [7.84675:84675]
B:BD[7.84675] → [7.84676:177406]
File deletion: simuscop-200-chr1-1.png
BF:BFD[5.13] → [6.139387:139441]
BF:BFD[6.139441] → [6.73022:73022]
B:BD[6.73022] → [6.73023:139386]
File deletion: haplotype-missing-2.png
BF:BFD[5.13] → [8.85115:85169]
BF:BFD[8.85169] → [8.42558:42558]
B:BD[8.42558] → [8.42559:85114]
File deletion: test-nointersect-chr15.png
BF:BFD[5.13] → [7.84616:84673]
BF:BFD[7.84673] → [7.78:78]
B:BD[7.78] → [7.79:84615]
File deletion: simuscop-error.png
BF:BFD[5.13] → [2.76997:77046]
BF:BFD[2.77046] → [2.5:5]
B:BD[2.5] → [2.6:76996]

File deletion: .hypb

BF:BFD[5.13] → [9.75203:75232]

BF:BFD[9.75232] → [9.74903:74903]

B:BD[9.74903] → [9.74904:74920]

∅:D[10.9766] → [9.74920:75202]

B:BD[9.74920] → [9.74920:75202]

B:BD[9.74920] → [10.9232:9766]


"bisonex.org"
("runs.waiting" nil nil find-file-other-window ("/ssh:meso:/Home/Users/apraga/runs.waiting" t) "alex@gentoo" "20231007:13:31:21" nil nil)
("samples.csv" nil nil find-file-other-window ("/ssh:meso:/Work/Users/apraga/bisonex/samples.csv" t) "alex@gentoo" "20231007:13:30:53" nil nil)
("biblio_appel_variant" nil nil link-to-file ("../../research/bisonex/thesis/biblio.org" 55515) "alex@laptop" "20231013:15:40:18" nil nil)
("appel_variant" nil nil link-to-file ("../../research/bisonex/thesis/pipeline.org" 21153) "alex@laptop" "20231013:15:38:35" nil nil)
("aligneur" nil nil link-to-file ("../../research/bisonex/thesis/pipeline.org" 1777) "alex@laptop" "20231013:15:14:20" nil nil)
("biblio_aligneur" nil nil link-to-file ("../../research/bisonex/thesis/biblio.org" 3417) "alex@laptop" "20231013:15:00:34" nil nil)

File deletion: simuscop-200-chr1-2.png
BF:BFD[5.13] → [6.72966:73020]
BF:BFD[6.73020] → [6.6:6]
B:BD[6.6] → [6.7:72965]
File deletion: haplotype-missing.png
BF:BFD[5.13] → [8.42504:42556]
BF:BFD[8.42556] → [8.10:10]
B:BD[8.10] → [8.11:42503]
File deletion: reads.png
BF:BFD[5.13] → [11.36100:36140]
BF:BFD[11.36140] → [11.14:14]
B:BD[11.14] → [11.15:36099]

File deletion: bisonex.org_archive

BF:BFD[5.13] → [12.4594:4637]

BF:BFD[12.4637] → [12.272:272]

B:BD[12.272] → [12.273:4592]

∅:D[13.854] → [12.4592:4593]

B:BD[12.4592] → [12.4592:4593]

B:BD[12.4593] → [13.855:1545]

B:BD[13.1545] → [11.36142:37425]

∅:D[11.37425] → [13.1545:1555]

B:BD[13.1545] → [13.1545:1555]

B:BD[13.1555] → [11.37426:44625]

B:BD[12.4592] → [13.378:854]

#    -*- mode: org -*-
Archived entries from file /home/alex/org/projects/bisonex.org
* DONE Vérifier qualité données sur mesocentre
CLOSED: [2023-01-12 Thu 15:48]
:PROPERTIES:
:ARCHIVE_TIME: 2023-01-12 Thu 15:48
:ARCHIVE_FILE: ~/org/projects/bisonex.org
:ARCHIVE_OLPATH: Données
:ARCHIVE_CATEGORY: bisonex
:ARCHIVE_TODO: DONE
:END:
** DONE BAM
CLOSED: [2023-01-12 Thu 15:47]
picard ValidateSamFile
On regarde juste le code d'erreur (0 = pas d'erreur)
** DONE Fastq
CLOSED: [2023-01-12 Thu 15:48]
fastqc
Il faut ensuite extraire les zip and chercher les erreur dedans
* KILL Implémenter d’autres pipeline
CLOSED: [2023-01-15 Sun 12:03]
:PROPERTIES:
:ARCHIVE_TIME: 2023-01-15 Sun 12:03
:ARCHIVE_FILE: ~/org/projects/bisonex.org
:ARCHIVE_CATEGORY: bisonex
:ARCHIVE_TODO: KILL
:END:
Voir https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04407-x
** KILL GATK
CLOSED: [2022   -11-11 Fri 20:01]
https://broadinstitute.github.io/warp/docs/Pipelines/Exome_Germline_Single_Sample_Pipeline/README
A priori, respecte les bonnes pratiques
** KILL Essayer snmake avec bonne pratiques
https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling/blob/main/.github/workflows/main.yml
Installer Mamba (micromamba ne fonctionne pas sous nix)
Ne fonctionne pas sous WSL2... MultiQC n’est pas assez à jour
Problèmes de versions...
** KILL Sarek
CLOSED: [2022-12-11 Sun 11:09]
*** Dépendences
**** Nix
#+begin_src sh
 nix profile install nixpkgs#mosdepth nixpkgs#python3
  nix-shell -p python310Packages.pyyaml --run "nextflow run nf-core/sarek -profile test --executor slurm --queue smp --outdir test -resume"
#+end_src
***** KILL derivation nix pour profile complet
CLOSED: [2022-12-11 Sun 11:09]
**** KILL Sans nix
CLOSED: [2022-09-24 Sat 10:20]
On utilise conda
#+begin_src sh
module unload nix
module load anaconda3@2021.05/gcc-12.1.0
module load nextflow@22.04.0/gcc-12.1.0
module load openjdk@11.0.14.1_1/gcc-12.1.0
nextflow run nf-core/sarek -profile conda,test --executor slurm --queue smp --outdir test -resume
#+end_src
Essai 1: erreurs de permissions, corrigé en relancant le programme
#+begin_quote
  Failed to create Conda environment
  command: conda create --mkdir --yes --quiet --prefix /Work/Users/apraga/test-sarek/work/conda/env-2d53b1db50de676670cf1a91ef0cf6db bioconda::tabix=1.11
  status : 1
  message:
    NotWritableError: The current user does not have write permissions to a required path.
      path: /Home/Users/apraga/.conda/pkgs/urls.txt
      uid: 1696
      gid: 513
    If you feel that permissions on this path are set incorrectly, you can manually
    change them by executing
      $ sudo chown 1696:513 /Home/Users/apraga/.conda/pkgs/urls.txt
#+end_quote
Corrigé avec
#+begin_src sh
      chown 1696:513 /Home/Users/apraga/.conda/pkgs/urls.txt
#+end_src
Mais problème de proxy
*** KILL Dérivation nix pour modules python
CLOSED: [2022-12-11 Sun 11:09]
*** KILL Lancer sarek en mode test
CLOSED: [2022-12-11 Sun 11:09]
#+begin_src sh
  nix-shell -p python310Packages.pyyaml --run "nextflow run nf-core/sarek -profile test --executor slurm --queue smp --outdir test -resume"
#+end_src
*** KILL Lancer sarek sur données allégées
CLOSED: [2022-12-11 Sun 11:09]
* DONE Essai 1
CLOSED: [2023-02-13 Mon 11:50]
:PROPERTIES:
:ARCHIVE_TIME: 2023-02-14 Tue 10:42
:ARCHIVE_FILE: ~/org/projects/bisonex.org
:ARCHIVE_OLPATH: Nouveau workflow/Dépendences avec Nix/hap.py/Faire fonctionner Tests
:ARCHIVE_CATEGORY: bisonex
:ARCHIVE_TODO: DONE
:END:
Problème avec chemin python pour pysam : Tools/__init__.py échoue mais on peut utilise build/bin/hap.py
#+begin_src
nix develop .#hap-py
$ genericBuild
#+end_src
On lance donc les tests à la main (trop d'erreurs sur les chemins)
#+begin_src
# OK !
HCDIR=build/bin build/bin/test_haplotypes
# OK !
bash src/sh/make_hg19.sh
HCDIR=build/bin HG19=hg19.fa bash src/sh/run_multimer
ge_test.sh
#+end_src
Écheck sur
$ HCDIR=build/bin bash src/sh/run_hapenum_test.sh
Traceback (most recent call last):
  File "build/bin/hap.py", line 26, in <module>
    import pysam
  File "/nix/store/3w2v5cl4x6ddq4281awcab9412r5gkaw-python3-3.10.9-env/lib/python3.10/site-packages/pysam/__init__.py", line 4, in <module>
    from pysam.libchtslib import *
ImportError: No module named libchtslib
IL faut commenter detect var
Une minorité concerne des problème d'haploides
❯ awk '!/^#/ && $10~/:FN:/ && $11!~/NOCALL/ && $10~/SNP/' test-allchr.vcf
304
avec 1/3 où l'exome manque une allèles
❯ awk '!/^#/ && $10~/:FN:/ && $11!~/NOCALL/ && $10~/SNP/ && $10~/homalt/' test-allchr.vcf  | wc -l
101
et 2/3 où il y a une allèle "en trop"
La majorité ne sont pas vu
❯ awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/' test-allchr.vcf  | wc -l
6361
Nombre de reads pour chaque position en bash (!)
#+begin_src bash
 awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/ {print $1":"$2"-"$2}' test-allchr.vcf  |  xargs -I {} sh -c 'echo -n {}";"; samtools view ../NA12878_NIST.b
am {} | wc -l' > count.csv
#+end_src
* KILL Julia
CLOSED: [2023-03-13 lun. 11:11]
:PROPERTIES:
:ARCHIVE_TIME: 2023-03-13 lun. 15:52
:ARCHIVE_FILE: c:/Users/apraga/org/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Validation : NA12878/GIAB/Exons seuls/D'où vient la différence ?/Statistiques
:ARCHIVE_CATEGORY: GIAB
:ARCHIVE_TODO: KILL
:END:
Conflict BAM et vcf
#+begin_src julia
using GeneticVariation
reader = VCF.Reader(open("../out/test-bed/test-allchr.vcf", "r"))
fn = 0
notSeen = 0
missingAllel = 0
surnumAllel = 0
for record in reader
    global fn, notSeen
    global missingAllel, surnumAllel
    if VCF.genotype(record)[1][2] == "FN" && VCF.genotype(record)[1][5] == "SNP"
        # println(record)
        # println("$(VCF.chrom(record))  $(VCF.pos(record))")
        fn = fn +1
        if VCF.genotype(record)[2][5] == "NOCALL"
            notSeen = notSeen + 1
        else
            if VCF.genotype(record)[1][6] == "homalt"
                missingAllel = missingAllel + 1
            elseif VCF.genotype(record)[2][6] == "homalt"
                surnumAllel = surnumAllel + 1
            end
        end
    end
end
close(reader)
println("SNP: false negative $fn")
println("SNP: not seen $notSeen")
println("SNP: missing allel $missingAllel")
println("SNP: surnumeraries allel $surnumAllel")
#+end_src
SNP: false negative 6665
SNP: not seen 6361
SNP: missing allel 101
SNP: surnumeraries allel 203
1. On confirme le nombre de SNP.
2. Une minorité concerne des problème d'haploides avec
   - 1/3 où l'exome manque une allèles
   - 2/3 où il y a une allèle "en trop"
3. La majorité ne sont pas vu (6361)
Nombre de reads pour chaque position en bash (!)
#+begin_src bash
 awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/ {print $1":"$2"-"$2}' test-allchr.vcf  |  xargs -I {} sh -c 'echo -n {}";"; samtools view ../NA12878_NIST.b
am {} | wc -l' > count.csv
* KILL Reads en dehors des exons
CLOSED: [2023-03-09 Thu 22:43]
:PROPERTIES:
:ARCHIVE_TIME: 2023-03-13 lun. 15:55
:ARCHIVE_FILE: c:/Users/apraga/org/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Validation : NA12878/GIAB/Exons seuls/D'où vient la différence ?/Statistiques
:ARCHIVE_CATEGORY: GIAB
:ARCHIVE_TODO: KILL
:END:
Ça a l'air sur des exemples simples ...
#+begin_src sh
wget https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.gff.gz
awk '/BestRefSeq\texon/ && /transcript_id=NM/ {print $1"\t"$4"\t"$5;}' GRCh38_latest_genomic.gff | grep ^NC | save exons.csv
#+end_src
#+begin_src julia
using CSV, DataFrames, Intervals
# Check the number of reads for each false negative (stored in count.csv)
# from hap.py output:
# awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/ {print $1":"$2"-"$2}' test-allchr.vcf  |  xargs -I {} sh -c 'echo -n {}";"; samtools view ../NA12878_NIST.b am {} | wc -l' > count.csv
function groupedCount(fname)
    f = DataFrame(CSV.File(fname, header=false))
    transform!(f, :Column1 => ByRow(x -> string.(split(x, ":"))[1]) => :chrom)
    transform!(f, :Column1 => ByRow(x -> parse(Int64, string.(split(x, "-"))[2])) => :pos)
    select!(f, Not([:Column1]))
    rename!(f, :Column2 => :nb)
    groupby(f, :chrom)
end
function groupedExons(fname)
    f = DataFrame(CSV.File(fname, header=["chrom", "start", "end"], delim="\t"))
    transform!(f, [:start, :end] => ByRow((x,y) -> Interval(x, y)) => :interval)
    select!(f, Not([:start, :end]))
    groupby(f, :chrom)
end
# Check is position x is in exons for chromosome chr
function isExon(x, exons, chr)
    # Remove duplicates
    exonsU = unique(exons[chr])
    res = transform(exonsU, :interval => ByRow(z -> x in z) => :check)
    # Result only found interval
    found = res[res.check,:].interval
    isempty(found) ? missing : first(found)
end
reads = groupedCount("../NA12878/happy/count.csv")
exons = groupedExons("exons.csv")
for g in range(1, size(reads)[1])
    local found
    found = transform(reads[g], :pos => ByRow(x -> isExon(x, exons, g)) => :exon)
    readsMissing = found[ismissing.(found.exon), :]
    # print("$(k.chrom):")
    print(g)
    print(": $(size(reads[g])[1]) reads, ")
    println("$(size(readsMissing)[1]) not in exons")
end
#+end_src
1: 448 reads, 64 not in exons
2: 307 reads, 47 not in exons
3: 228 reads, 37 not in exons
4: 175 reads, 28 not in exons
5: 237 reads, 38 not in exons
6: 1223 reads, 304 not in exons
7: 274 reads, 52 not in exons
8: 414 reads, 41 not in exons
9: 161 reads, 47 not in exons
10: 194 reads, 37 not in exons
11: 304 reads, 39 not in exons
12: 254 reads, 32 not in exons
13: 168 reads, 120 not in exons
14: 184 reads, 26 not in exons
15: 250 reads, 90 not in exons
16: 239 reads, 29 not in exons
17: 373 reads, 35 not in exons
18: 85 reads, 17 not in exons
19: 576 reads, 46 not in exons
20: 83 reads, 22 not in exons
21: 67 reads, 14 not in exons
22: 117 reads, 24 not in exons
* KILL Répartition par chromosome: variable mais seul le 6 = hotspot
CLOSED: [2023-03-07 Tue 22:44]
:PROPERTIES:
:ARCHIVE_TIME: 2023-03-13 lun. 15:55
:ARCHIVE_FILE: c:/Users/apraga/org/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Validation : NA12878/GIAB/Exons seuls/D'où vient la différence ?/Statistiques
:ARCHIVE_CATEGORY: GIAB
:ARCHIVE_TODO: KILL
:END:
#+begin_src julia
using CSV, DataFrames
f = DataFrame(CSV.File("count.csv", header=false))
size(f[f.Column2 .< 10,:])
#+end_src
(4430, 2)
#+begin_src julia
using CSV, DataFrames
function cleanCount(fname)
    f = DataFrame(CSV.File(fname, header=false))
    transform!(f, :Column1 => ByRow(x -> string.(split(x, ":"))[1]) => :chrom)
    transform!(f, :Column1 => ByRow(x -> string.(split(x, "-"))[2]) => :pos)
    select!(f, Not([:Column1]))
    rename!(f, :Column2 => :nb)
end
f = cleanCount("count.csv")
grouped = groupby(f, :chrom)
for (k, g) in pairs(grouped)
    println("$(k.chrom): $(size(g, 1))")
end
#+end_src
#+RESULTS:
: NC_000001.11: 448
: NC_000002.12: 307
: NC_000003.12: 228
: NC_000004.12: 175
: NC_000005.10: 237
: NC_000006.12: 1223
: NC_000007.14: 274
: NC_000008.11: 414
: NC_000009.12: 161
: NC_000010.11: 194
: NC_000011.10: 304
: NC_000012.12: 254
: NC_000013.11: 168
: NC_000014.9: 184
: NC_000015.10: 250
: NC_000016.10: 239
: NC_000017.11: 373
: NC_000018.10: 85
: NC_000019.10: 576
: NC_000020.11: 83
: NC_000021.9: 67
: NC_000022.11: 117
* KILL Awk
CLOSED: [2023-03-12 Sun 22:12]
:PROPERTIES:
:ARCHIVE_TIME: 2023-03-13 lun. 15:55
:ARCHIVE_FILE: c:/Users/apraga/org/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Validation : NA12878/GIAB/Exons seuls/D'où vient la différence ?/Statistiques
:ARCHIVE_CATEGORY: GIAB
:ARCHIVE_TODO: KILL
:END:
NB: awk car bcftools query ne semble pas prendre en compte les nouvelles colonnes
On confirnme le nombre de SNP:
❯ awk '!/^#/ && $10~/:FN:/ && $10~/SNP/' test-allchr.vcf  | wc -l
6665
Une minorité concerne des problème d'haploides
❯ awk '!/^#/ && $10~/:FN:/ && $11!~/NOCALL/ && $10~/SNP/' test-allchr.vcf
304
avec 1/3 où l'exome manque une allèles
❯ awk '!/^#/ && $10~/:FN:/ && $11!~/NOCALL/ && $10~/SNP/ && $10~/homalt/' test-allchr.vcf  | wc -l
101
et 2/3 où il y a une allèle "en trop"
La majorité ne sont pas vu
❯ awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/' test-allchr.vcf  | wc -l
6361
Nombre de reads pour chaque position en bash (!)
#+begin_src bash
 awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/ {print $1":"$2"-"$2}' test-allchr.vcf  |  xargs -I {} sh -c 'echo -n {}";"; samtools view ../NA12878_NIST.b
am {} | wc -l' > count.csv
#+end_src
* KILL Comprendre/améliorer Recall SNP 0.855
CLOSED: [2023-03-13 lun. 15:55] SCHEDULED: <2023-03-04 Sat>
:PROPERTIES:
:ARCHIVE_TIME: 2023-03-13 lun. 15:55
:ARCHIVE_FILE: c:/Users/apraga/org/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Validation : NA12878/GIAB/Exons seuls/D'où vient la différence ?/Statistiques
:ARCHIVE_CATEGORY: GIAB
:ARCHIVE_TODO: KILL
:END:
 on est inférieur à Kumaran et al 2019
** KILL Regarder les FN (SNP)
CLOSED: [2023-03-13 lun. 15:55] SCHEDULED: <2023-03-04 Sat  >
*** Manuel:
NC_000001.11:1385919 pas de read 1/1:FN:.:i1_5:INDEL:homalt:.
NC_000001.11:1623412 1 read     1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1668449 33 read sur 160 voient l'allèle alternative 1/1:FN:am:ti:SNP:homalt:.
NC_000001.11:1676135 67 reads, non vu 0/1:FN:.:ti:SNP:het:.
NC_000001.11:1734812 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1745808 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1745814 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1953616 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:2512975 0/1:FN:.:ti:SNP:het:
* DONE Awk
CLOSED: [2023-03-12 Sun 22:12]
:PROPERTIES:
:ARCHIVE_TIME: 2023-03-12 Sun 22:19
:ARCHIVE_FILE: ~/org/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Validation : NA12878/GIAB/Exons seuls/D'où vient la différence ?/Statistiques
:ARCHIVE_CATEGORY: GIAB
:ARCHIVE_TODO: DONE
:END:
NB: awk car bcftools query ne semble pas prendre en compte les nouvelles colonnes
On confirnme le nombre de SNP:
❯ awk '!/^#/ && $10~/:FN:/ && $10~/SNP/' test-allchr.vcf  | wc -l
6665

File deletion: ophn1.bib, ophn1.bib, ophn1.md, ophn1.org, ophn1.md

BFD:BFD[14.29] → [14.708:741]

BF:BFD[14.741] → [16.168:168]

BFD:BFD[4.2] → [16.3257:3290]

BF:BFD[16.3290] → [16.168:168]

BF:BFD[4.2] → [17.6906:6938]

BF:BFD[17.6938] → [16.168:168]

BFD:BFD[14.29] → [15.51201:51234]

BF:BFD[15.51234] → [16.168:168]

BFD:BFD[14.29] → [18.111135:111167]

BF:BFD[18.111167] → [16.168:168]

B:BD[16.168] → [18.111168:111179]

∅:D[15.51254] → [16.169:3256]

∅:D[18.111179] → [16.169:3256]

B:BD[16.168] → [16.169:3256]

B:BD[16.3256] → [18.111180:111184]

``` bibtex
@article{cvetkovska2021,
title = {Ophn1 regulation of prefrontal inhibition: A mechanism for stress susceptibility in intellectual disability},
journal = {Neuron},
volume = {109},
number = {10},
pages = {1583-1584},
year = {2021},
issn = {0896-6273},
doi = {https://doi.org/10.1016/j.neuron.2021.04.030},
url = {https://www.sciencedirect.com/science/article/pii/S0896627321003263},
author = {Vedrana Cvetkovska and Rosemary C. Bagot},
abstract = {Wang et al. (2021) characterize the molecular, cellular, and circuit-level role of Oligophrenin-1 in prefrontal parvalbumin interneurons, demonstrating that loss of Ophn1 function in these neurons is a mechanism for increased susceptibility to stress in intellectual disability caused by OPHN1 mutations.}
}
@article{nuovo2021,
author = {Nuovo, Sara and Brankovic, Vesna and Caputi, Caterina and Casella, Antonella and Nigro, Vincenzo and Leuzzi, Vincenzo and Valente, Enza Maria},
title = {Novel unconventional variants expand the allelic spectrum of OPHN1 gene},
journal = {American Journal of Medical Genetics Part A},
volume = {185},
number = {5},
pages = {1575-1581},
keywords = {allelic spectrum, BAR domain, oligophrenin, OPHN1, proline-rich domain},
doi = {https://doi.org/10.1002/ajmg.a.62144},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.62144},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/ajmg.a.62144},
abstract = {Abstract Mutations in the OPHN1 gene cause a rare X-linked recessive neurodevelopmental disorder characterized by intellectual disability, variably associated with cerebellar hypoplasia and distinctive facial appearance. In most of cases so far reported, the identified genomic variants involve the region encoding the central RhoGAP domain of the oligophrenin-1 protein, and are predicted to result in a complete loss of function. By using a NGS-based diagnostic approach, we identified three male and a female patients from two unrelated families carrying novel non-disruptive OPHN1 variants (the in-frame c.116\_127 deletion and the missense c.2129C>T change, respectively), affecting either the BAR domain or the C-terminus proline-rich domain of the protein. Clinical and neuroimaging findings in the patients recapitulated the main features of OPHN1-related syndrome, including developmental delay, intellectual disability, behavioral disorder, dysmorphic features, seizures, cerebellar hypoplasia, and ventriculomegaly. Yet, we observed a wide variability even among affected siblings, confirming the lack of clear genotype–phenotype correlation. Our results expand the allelic spectrum of OPHN1 and illustrate the challenges for clinical interpretation of non-disruptive variants affecting X-linked genes.},
year = {2021}
}
@article{boglics2020,
  title={Exon 21 deletion in the OPHN1 gene in a family with syndromic X-linked intellectual disability: Case report},
  author={Bogli{\c{s}}, Alina and Cosma, Adriana S and Tripon, Florin and B{\~a}nescu, Claudia},
  journal={Medicine},
  volume={99},
  number={33},
  year={2020},
  publisher={Wolters Kluwer Health}
}
```

Replacement in lists/series.md at line 1 [18.12657]

B:BD[18.12657] → [18.12658:12987]

-   [ ] Big Bang Theory: Saison 1
-   [ ] Breaking Bad: Saison 1,2
-   [x] Deadwood
-   [ ] Dexter: saison 1
-   [ ] Elementary: saison 1-4
-   [ ] Good Eats: saison 1,2
-   [ ] Lost: saison 1-3
-   [x] Mythbusters
-   [ ] Planet Earth: Season 1
-   [ ] Savage builds: Season 1
-   [x] Rome
-   [x] Sherlock (2010)
-   [x] Weeds

[18.12657]

-  [ ] Big Bang Theory: Saison 1
-  [ ] Breaking Bad: Saison 1,2
-  [x] Deadwood
-  [ ] Dexter: saison 1
-  [ ] Elementary: saison 1-4
-  [ ] Good Eats: saison 1,2
-  [ ] Lost: saison 1-3
-  [x] Mythbusters
-  [ ] Planet Earth: Season 1
-  [ ] Savage builds: Season 1
-  [x] Rome
-  [x] Sherlock (2010)
-  [x] Weeds

Replacement in lists/movies.md at line 1 [18.366669]
B:BD[18.366669] → [19.32379:32385]
```
# Vu 
```
[18.366669]
[18.366756]
```
---
title: Films
---
```
Insertion in lists/comics.md at line 1 [18.451678]
[18.451678]
[18.451679]
```
---
title: Comics
---
```
Deletion in lists/comics.md at line 6 [18.451678]
B:BD[18.451684] → [18.451684:451685]

Replacement in lists/comics.md at line 7 [18.451678]

B:BD[18.451695] → [18.451695:454499]


### [TODO]{.todo .TODO} Batman : City of owls (8-12) Batman & Robin : first arc (1-17) {#batman-city-of-owls-8-12-batman-robin-first-arc-1-17}
### [TODO]{.todo .TODO} Batman : The court of owls (1-7) Batman - Year Two Detective comic {#batman-the-court-of-owls-1-7-batman---year-two-detective-comic}
### [TODO]{.todo .TODO} Hush Incorporated : The Demon Star (1-13) {#hush-incorporated-the-demon-star-1-13}
### [DONE]{.done .DONE} Arkham Reborn {#arkham-reborn rating="3.5"}
### [DONE]{.done .DONE} Bane of the Demon {#bane-of-the-demon rating="3.5"}
### [DONE]{.done .DONE} Batman and the Mad Monk {#batman-and-the-mad-monk rating="3"}
### [DONE]{.done .DONE} Batman and the Monster Men {#batman-and-the-monster-men}
### [DONE]{.done .DONE} Batman & Danger Girl {#batman-danger-girl rating="3.5"}
### [DONE]{.done .DONE} Batman & Deadman : Death and Glory {#batman-deadman-death-and-glory rating="3.5"}
### [DONE]{.done .DONE} Batman Family (2002) {#batman-family-2002 rating="4"}
### [DONE]{.done .DONE} Batman & Green Arrow : The Poison Tomorrow {#batman-green-arrow-the-poison-tomorrow rating="3.5"}
### [DONE]{.done .DONE} Batman/Hellboy/Starman :PROPERTIES::rating: 3.5 [[END]{.smallcaps}]{.tag tag-name="END"} {#batmanhellboystarman-propertiesrating-3.5}
### [DONE]{.done .DONE} Batman Last Rites - The Butler {#batman-last-rites---the-butler rating="3"}
### [DONE]{.done .DONE} Batman Huntress & Spoiler - Blunt Trauma {#batman-huntress-spoiler---blunt-trauma rating="3.5"}
### [DONE]{.done .DONE} Batman & Tarzan : Claws of the Cat-Woman {#batman-tarzan-claws-of-the-cat-woman}
### [DONE]{.done .DONE} Batman - Year One {#batman---year-one rating="4.5"}
### [DONE]{.done .DONE} Battle for the Cowl {#battle-for-the-cowl rating="3.5"}
### [DONE]{.done .DONE} Bruce - The road home {#bruce---the-road-home rating="3.5"}
### [DONE]{.done .DONE} Bruce Wayne : Fugitive {#bruce-wayne-fugitive rating="3.5"}
### [DONE]{.done .DONE} Bruce Wayne : Murderer {#bruce-wayne-murderer rating="4"}
### [DONE]{.done .DONE} Catwoman - Follow the Money {#catwoman---follow-the-money rating="3.5"}
### [DONE]{.done .DONE} Catwoman - Tail of the Gun {#catwoman---tail-of-the-gun rating="4"}
### [DONE]{.done .DONE} Catwoman - When in Rome {#catwoman---when-in-rome rating="3.5"}
### [DONE]{.done .DONE} Deathblow {#deathblow rating="4"}
### [DONE]{.done .DONE} Huntress - Cry for blood {#huntress---cry-for-blood rating="3.5"}
### [DONE]{.done .DONE} Batman Last Rites - Last days of Gotham {#batman-last-rites---last-days-of-gotham rating="3"}
### [DONE]{.done .DONE} The Dark Knight returns {#the-dark-knight-returns rating="4.5"}
### [DONE]{.done .DONE} The Killing Joke {#the-killing-joke rating="4.5"}
### [DONE]{.done .DONE} The Long Halloween {#the-long-halloween rating="4.5"}

[18.451695]

[18.454499]

- [ ] Batman : City of owls (8-12) Batman & Robin : first arc (1-17) {#batman-city-of-owls-8-12-batman-robin-first-arc-1-17}
- [ ] Batman : The court of owls (1-7) Batman - Year Two Detective comic {#batman-the-court-of-owls-1-7-batman---year-two-detective-comic}
- [ ] Hush Incorporated : The Demon Star (1-13) {#hush-incorporated-the-demon-star-1-13}
- [X] Arkham Reborn {#arkham-reborn rating="3.5"}
- [X] Bane of the Demon {#bane-of-the-demon rating="3.5"}
- [X] Batman and the Mad Monk {#batman-and-the-mad-monk rating="3"}
- [X] Batman and the Monster Men {#batman-and-the-monster-men}
- [X] Batman & Danger Girl {#batman-danger-girl rating="3.5"}
- [X] Batman & Deadman : Death and Glory {#batman-deadman-death-and-glory rating="3.5"}
- [X] Batman Family (2002) {#batman-family-2002 rating="4"}
- [X] Batman & Green Arrow : The Poison Tomorrow {#batman-green-arrow-the-poison-tomorrow rating="3.5"}
- [X] Batman/Hellboy/Starman :PROPERTIES::rating: 3.5 [[END]{.smallcaps}]{.tag tag-name="END"} {#batmanhellboystarman-propertiesrating-3.5}
- [X] Batman Last Rites - The Butler {#batman-last-rites---the-butler rating="3"}
- [X] Batman Huntress & Spoiler - Blunt Trauma {#batman-huntress-spoiler---blunt-trauma rating="3.5"}
- [X] Batman & Tarzan : Claws of the Cat-Woman {#batman-tarzan-claws-of-the-cat-woman}
- [X] Batman - Year One {#batman---year-one rating="4.5"}
- [X] Battle for the Cowl {#battle-for-the-cowl rating="3.5"}
- [X] Bruce - The road home {#bruce---the-road-home rating="3.5"}
- [X] Bruce Wayne : Fugitive {#bruce-wayne-fugitive rating="3.5"}
- [X] Bruce Wayne : Murderer {#bruce-wayne-murderer rating="4"}
- [X] Catwoman - Follow the Money {#catwoman---follow-the-money rating="3.5"}
- [X] Catwoman - Tail of the Gun {#catwoman---tail-of-the-gun rating="4"}
- [X] Catwoman - When in Rome {#catwoman---when-in-rome rating="3.5"}
- [X] Deathblow {#deathblow rating="4"}
- [X] Huntress - Cry for blood {#huntress---cry-for-blood rating="3.5"}
- [X] Batman Last Rites - Last days of Gotham {#batman-last-rites---last-days-of-gotham rating="3"}
- [X] The Dark Knight returns {#the-dark-knight-returns rating="4.5"}
- [X] The Killing Joke {#the-killing-joke rating="4.5"}
- [X] The Long Halloween {#the-long-halloween rating="4.5"}

Replacement in lists/comics.md at line 38 [18.451678]

B:BD[18.454512] → [18.454512:455734]


### [DONE]{.done .DONE} Brainiac {#brainiac rating="4.5"}
### [DONE]{.done .DONE} Earth One Vol. 1 and 2 {#earth-one-vol.-1-and-2 rating="3.5"}
### [DONE]{.done .DONE} Escape from Bizarro World {#escape-from-bizarro-world rating="3.5"}
### [DONE]{.done .DONE} For All Seasons {#for-all-seasons rating="4.5"}
### [DONE]{.done .DONE} For The Man Who Has Everything {#for-the-man-who-has-everything rating="4.5"}
### [DONE]{.done .DONE} Kingdom Come {#kingdom-come rating="4.5"}
### [DONE]{.done .DONE} Last Son {#last-son rating="3.5"}
### [DONE]{.done .DONE} Peace on Earth {#peace-on-earth rating="3.5"}
### [DONE]{.done .DONE} Red Son {#red-son rating="3.5"}
### [DONE]{.done .DONE} Secret Identity {#secret-identity rating="4.5"}
### [DONE]{.done .DONE} Superman and the Legion of Super Heroes {#superman-and-the-legion-of-super-heroes rating="3.5"}
### [DONE]{.done .DONE} What\'s So Funny About Truth, Justice and the American Way? {#whats-so-funny-about-truth-justice-and-the-american-way rating="3.5"}
### [DONE]{.done .DONE} Whatever Happened to the Man of Tomorrow? {#whatever-happened-to-the-man-of-tomorrow rating="4.5"}
### [DONE]{.done .DONE} Superman in Exile {#superman-in-exile rating="3.5"}

[18.454512]

[18.455734]

- [X] Brainiac {#brainiac rating="4.5"}
- [X] Earth One Vol. 1 and 2 {#earth-one-vol.-1-and-2 rating="3.5"}
- [X] Escape from Bizarro World {#escape-from-bizarro-world rating="3.5"}
- [X] For All Seasons {#for-all-seasons rating="4.5"}
- [X] For The Man Who Has Everything {#for-the-man-who-has-everything rating="4.5"}
- [X] Kingdom Come {#kingdom-come rating="4.5"}
- [X] Last Son {#last-son rating="3.5"}
- [X] Peace on Earth {#peace-on-earth rating="3.5"}
- [X] Red Son {#red-son rating="3.5"}
- [X] Secret Identity {#secret-identity rating="4.5"}
- [X] Superman and the Legion of Super Heroes {#superman-and-the-legion-of-super-heroes rating="3.5"}
- [X] What\'s So Funny About Truth, Justice and the American Way? {#whats-so-funny-about-truth-justice-and-the-american-way rating="3.5"}
- [X] Whatever Happened to the Man of Tomorrow? {#whatever-happened-to-the-man-of-tomorrow rating="4.5"}
- [X] Superman in Exile {#superman-in-exile rating="3.5"}

Deletion in lists/comics.md at line 53 [18.451678]
B:BD[18.455743] → [18.455743:455744]

Replacement in lists/comics.md at line 54 [18.451678]

B:BD[18.455757] → [18.455757:457405]


### [DONE]{.done .DONE} Ultimate Adventures (1-6) {#ultimate-adventures-1-6}
### [DONE]{.done .DONE} Ultimates 3 {#ultimates-3 rating="3.5"}
### [DONE]{.done .DONE} Ultimate Galactus {#ultimate-galactus}
### [DONE]{.done .DONE} READ Ultimate Nightmare {#read-ultimate-nightmare}
### [DONE]{.done .DONE} READ Ultimate Secret {#read-ultimate-secret}
### [DONE]{.done .DONE} READ Ultimate Vision {#read-ultimate-vision}
### [DONE]{.done .DONE} READ Ultimate Extinction {#read-ultimate-extinction}
### [DONE]{.done .DONE} Ultimate X4 {#ultimate-x4}
### [DONE]{.done .DONE} Ultimate War (After 025) {#ultimate-war-after-025}
### [DONE]{.done .DONE} Ultimate X-Men 1-97 {#ultimate-x-men-1-97 rating="3.5"}
### [DONE]{.done .DONE} Ultimate X-Men 98-100 {#ultimate-x-men-98-100 rating="3.5"}
### [DONE]{.done .DONE} Fantastic Four - X Men Annual {#fantastic-four---x-men-annual rating="2.5"}
### [DONE]{.done .DONE} Ultimate human {#ultimate-human rating="3"}
### [DONE]{.done .DONE} Ultimate origins {#ultimate-origins rating="3"}
### [DONE]{.done .DONE} Ultimate human {#ultimate-human-1 rating="3"}
### [DONE]{.done .DONE} Ultimate power {#ultimate-power rating="3"}
### [DONE]{.done .DONE} Ultimate Fantastic four 58-60 {#ultimate-fantastic-four-58-60 rating="3"}
### [DONE]{.done .DONE} Ultimate Spiderman 129-133 {#ultimate-spiderman-129-133 rating="3.5"}
### [DONE]{.done .DONE} Ultimate Spiderman : Requiem {#ultimate-spiderman-requiem rating="3"}
### [DONE]{.done .DONE} Ultimate X-men : Requiem {#ultimate-x-men-requiem rating="3"}
### [DONE]{.done .DONE} Ultimate Fantastic Four : Requiem {#ultimate-fantastic-four-requiem}

[18.455757]

- [X] Ultimate Adventures (1-6) {#ultimate-adventures-1-6}
- [X] Ultimates 3 {#ultimates-3 rating="3.5"}
- [X] Ultimate Galactus {#ultimate-galactus}
- [X] READ Ultimate Nightmare {#read-ultimate-nightmare}
- [X] READ Ultimate Secret {#read-ultimate-secret}
- [X] READ Ultimate Vision {#read-ultimate-vision}
- [X] READ Ultimate Extinction {#read-ultimate-extinction}
- [X] Ultimate X4 {#ultimate-x4}
- [X] Ultimate War (After 025) {#ultimate-war-after-025}
- [X] Ultimate X-Men 1-97 {#ultimate-x-men-1-97 rating="3.5"}
- [X] Ultimate X-Men 98-100 {#ultimate-x-men-98-100 rating="3.5"}
- [X] Fantastic Four - X Men Annual {#fantastic-four---x-men-annual rating="2.5"}
- [X] Ultimate human {#ultimate-human rating="3"}
- [X] Ultimate origins {#ultimate-origins rating="3"}
- [X] Ultimate human {#ultimate-human-1 rating="3"}
- [X] Ultimate power {#ultimate-power rating="3"}
- [X] Ultimate Fantastic four 58-60 {#ultimate-fantastic-four-58-60 rating="3"}
- [X] Ultimate Spiderman 129-133 {#ultimate-spiderman-129-133 rating="3.5"}
- [X] Ultimate Spiderman : Requiem {#ultimate-spiderman-requiem rating="3"}
- [X] Ultimate X-men : Requiem {#ultimate-x-men-requiem rating="3"}
- [X] Ultimate Fantastic Four : Requiem {#ultimate-fantastic-four-requiem}

Insertion in lists/anime.md at line 1 [3.881]
[3.881]
[3.882]
```
---
title: Anime
---
```

Replacement in archive/bisonex.org_archive at line 7 [20.46128]

B:BD[20.46219] → [20.46219:46265]

* DONE NA12878
CLOSED: [2023-04-16 Sun 16:33]

[20.46219]

[20.46265]

* DONE Vérifier qualité données sur mesocentre
CLOSED: [2023-01-12 Thu 15:48]

Replacement in archive/bisonex.org_archive at line 10 [20.46128]
B:BD[20.46278] → [20.46278:46314]
```
:ARCHIVE_TIME: 2023-04-16 Sun 16:34
```
[20.46278]
[20.46314]
```
:ARCHIVE_TIME: 2023-01-12 Thu 15:48
```
Replacement in archive/bisonex.org_archive at line 12 [20.46128]
B:BD[20.46356] → [20.46356:46408]
```
:ARCHIVE_OLPATH: Nouveau workflow/Bases de données
```
[20.46356]
[20.46408]
```
:ARCHIVE_OLPATH: Données
```
Deletion in archive/bisonex.org_archive at line 15 [20.46128]
B:BD[20.46455] → [20.46455:46480]
```
:ARCHIVE_ITAGS: workflow
```

Replacement in archive/bisonex.org_archive at line 16 [20.46128]

B:BD[20.46486] → [20.46486:46869]

Doc: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/NA12878_HG001/latest/README_v4.2.1.txt
Bed : https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/NA12878_HG001/latest/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.bed
https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/NA12878_HG001/latest/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz

[20.46486]

[21.45307]

** DONE BAM
CLOSED: [2023-01-12 Thu 15:47]
picard ValidateSamFile
On regarde juste le code d'erreur (0 = pas d'erreur)
** DONE Fastq
CLOSED: [2023-01-12 Thu 15:48]
fastqc
Il faut ensuite extraire les zip and chercher les erreur dedans

Replacement in archive/bisonex.org_archive at line 25 [20.46128]

B:BD[21.45308] → [21.45308:45399]

* KILL Script maison :generate:
CLOSED: [2023-05-13 Sat 18:29] SCHEDULED: <2023-05-01 Mon>

[21.45308]

[21.45399]

* KILL Implémenter d’autres pipeline
CLOSED: [2023-01-15 Sun 12:03]

Replacement in archive/bisonex.org_archive at line 28 [20.46128]

B:BD[21.45412] → [21.45412:45563]

:ARCHIVE_TIME: 2023-06-03 Sat 17:16
:ARCHIVE_FILE: ~/roam/personal/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Fastq avec tous les variants centogène

[21.45412]

[21.45563]

:ARCHIVE_TIME: 2023-01-15 Sun 12:03
:ARCHIVE_FILE: ~/org/projects/bisonex.org

Deletion in archive/bisonex.org_archive at line 32 [20.46128]
B:BD[21.45610] → [21.45610:45642]
```
:ARCHIVE_ITAGS: tests centogene
```

Replacement in archive/bisonex.org_archive at line 33 [20.46128]

B:BD[21.45648] → [21.45648:46099]

** KILL SNV
CLOSED: [2023-05-13 Sat 18:29] SCHEDULED: <2023-05-01 Mon>
*** DONE Script python: ok seulement pour reads corrigé, trop long sinon
CLOSED: [2023-05-01 Mon 13:32]
Même sur un seul chromosome (15)...
*** DONE Couper les données avec bedtools intersect ?
CLOSED: [2023-05-01 Mon 20:33]
-wa pour avoir les reads qui corresponds
-v pour ceux qui n'intersecte pass
ok sur un exemple
**** DONE Test simple : ok
CLOSED: [2023-05-01 Mon 13:43]

[21.45648]

[21.46099]

Voir https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04407-x
** KILL GATK
CLOSED: [2022   -11-11 Fri 20:01]
https://broadinstitute.github.io/warp/docs/Pipelines/Exome_Germline_Single_Sample_Pipeline/README
A priori, respecte les bonnes pratiques
** KILL Essayer snmake avec bonne pratiques
https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling/blob/main/.github/workflows/main.yml
Installer Mamba (micromamba ne fonctionne pas sous nix)
Ne fonctionne pas sous WSL2... MultiQC n’est pas assez à jour
Problèmes de versions...
** KILL Sarek
CLOSED: [2022-12-11 Sun 11:09]
*** Dépendences
**** Nix
#+begin_src sh
 nix profile install nixpkgs#mosdepth nixpkgs#python3
  nix-shell -p python310Packages.pyyaml --run "nextflow run nf-core/sarek -profile test --executor slurm --queue smp --outdir test -resume"
#+end_src
***** KILL derivation nix pour profile complet
CLOSED: [2022-12-11 Sun 11:09]
**** KILL Sans nix
CLOSED: [2022-09-24 Sat 10:20]
On utilise conda
#+begin_src sh
module unload nix
module load anaconda3@2021.05/gcc-12.1.0
module load nextflow@22.04.0/gcc-12.1.0
module load openjdk@11.0.14.1_1/gcc-12.1.0
nextflow run nf-core/sarek -profile conda,test --executor slurm --queue smp --outdir test -resume
#+end_src
Essai 1: erreurs de permissions, corrigé en relancant le programme
#+begin_quote
  Failed to create Conda environment
  command: conda create --mkdir --yes --quiet --prefix /Work/Users/apraga/test-sarek/work/conda/env-2d53b1db50de676670cf1a91ef0cf6db bioconda::tabix=1.11
  status : 1
  message:
    NotWritableError: The current user does not have write permissions to a required path.
      path: /Home/Users/apraga/.conda/pkgs/urls.txt
      uid: 1696
      gid: 513

Replacement in archive/bisonex.org_archive at line 74 [20.46128]

B:BD[21.46100] → [21.46100:46406]

#+attr_html: :width 500px
[[./test-intersect-chr15.png]]
#+attr_html: :width 500px
[[./test-nointersect-chr15.png]]
**** DONE Chromosome 15 : vérifier BAM
CLOSED: [2023-05-01 Mon 20:33] SCHEDULED: <2023-05-01 Mon>
#+begin_src
samtools view -b `63003856_S135.bam`  NC_000015.10 > `63003856_S135_chr15.bam`

[21.46100]

[21.46406]

    If you feel that permissions on this path are set incorrectly, you can manually
    change them by executing
      $ sudo chown 1696:513 /Home/Users/apraga/.conda/pkgs/urls.txt
#+end_quote
Corrigé avec
#+begin_src sh
      chown 1696:513 /Home/Users/apraga/.conda/pkgs/urls.txt

Replacement in archive/bisonex.org_archive at line 83 [20.46128]

B:BD[21.46416] → [21.46416:46460]

On génère un python avec les dépendances

[21.46416]

[21.46460]

Mais problème de proxy
*** KILL Dérivation nix pour modules python
CLOSED: [2022-12-11 Sun 11:09]
*** KILL Lancer sarek en mode test
CLOSED: [2022-12-11 Sun 11:09]
#+begin_src sh
  nix-shell -p python310Packages.pyyaml --run "nextflow run nf-core/sarek -profile test --executor slurm --queue smp --outdir test -resume"
#+end_src
*** KILL Lancer sarek sur données allégées
CLOSED: [2022-12-11 Sun 11:09]
* DONE Essai 1
CLOSED: [2023-02-13 Mon 11:50]
:PROPERTIES:
:ARCHIVE_TIME: 2023-02-14 Tue 10:42
:ARCHIVE_FILE: ~/org/projects/bisonex.org
:ARCHIVE_OLPATH: Nouveau workflow/Dépendences avec Nix/hap.py/Faire fonctionner Tests
:ARCHIVE_CATEGORY: bisonex
:ARCHIVE_TODO: DONE
:END:
Problème avec chemin python pour pysam : Tools/__init__.py échoue mais on peut utilise build/bin/hap.py

Replacement in archive/bisonex.org_archive at line 105 [20.46128]
B:BD[21.46472] → [21.46472:46482]
```
nix-build
```
[21.46472]
[21.46482]
```
nix develop .#hap-py
$ genericBuild
```

Replacement in archive/bisonex.org_archive at line 108 [20.46128]

B:BD[21.46492] → [21.46492:46618]

Puis on lance un script julia qui va couper le bam en 2, lancer le script python sur l'intersection et fusionner le résultat

[21.46492]

[21.46618]


On lance donc les tests à la main (trop d'erreurs sur les chemins)

Replacement in archive/bisonex.org_archive at line 111 [20.46128]

B:BD[21.46630] → [21.46630:46718]

julia -Jbisonex.so --project=. insertVariants.jl `63003856_S135_chr15.bam` test_new.bam

[21.46630]

[21.46718]

# OK !
HCDIR=build/bin build/bin/test_haplotypes
# OK !
bash src/sh/make_hg19.sh
HCDIR=build/bin HG19=hg19.fa bash src/sh/run_multimer
ge_test.sh

Deletion in archive/bisonex.org_archive at line 119 [20.46128]
B:BD[21.46728] → [21.46728:46787]
```
NB: pour accélerer l'exécution, générer une sysimage :
```

Replacement in archive/bisonex.org_archive at line 120 [20.46128]

B:BD[21.46788] → [21.46788:46891]

#+begin_src julia
(1.7) pkg> activate .
julia> create_sysimage(; sysimage_path="bisonex.so")
#+end_src

[21.46788]

[21.46891]

Écheck sur
$ HCDIR=build/bin bash src/sh/run_hapenum_test.sh
Traceback (most recent call last):
  File "build/bin/hap.py", line 26, in <module>
    import pysam
  File "/nix/store/3w2v5cl4x6ddq4281awcab9412r5gkaw-python3-3.10.9-env/lib/python3.10/site-packages/pysam/__init__.py", line 4, in <module>
    from pysam.libchtslib import *
ImportError: No module named libchtslib
IL faut commenter detect var

Deletion in archive/bisonex.org_archive at line 130 [20.46128]
B:BD[21.46892] → [21.46892:46965]
```
3 variants: Ok sur le nombre de reads et les variants
Ok pour homozygote
```

Replacement in archive/bisonex.org_archive at line 131 [20.46128]

B:BD[21.46966] → [21.46966:47018]

#+attr_html: :width 500px
[[./check-snv-chr15.png]]

[21.46966]

[21.47018]

* DONE Awk
CLOSED: [2023-03-12 Sun 22:12]
:PROPERTIES:
:ARCHIVE_TIME: 2023-03-12 Sun 22:19
:ARCHIVE_FILE: ~/org/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Validation : NA12878/GIAB/Exons seuls/D'où vient la différence ?/Statistiques
:ARCHIVE_CATEGORY: GIAB
:ARCHIVE_TODO: DONE
:END:
NB: awk car bcftools query ne semble pas prendre en compte les nouvelles colonnes

Replacement in archive/bisonex.org_archive at line 142 [20.46128]

B:BD[21.47019] → [21.47019:51279]

**** DONE Chromosome 15 Vérifier VAF avec checkBam.jl: ok
julia> @subset snv :chrom .== "NC_000015.10"
26×10 DataFrame
 Row │ chrom         pos       variant        variantType  zygosity      ref        alt        refCount  altCount  readsCount
     │ SubStrin…?    Int64     SubStrin…?     String?      String15      SubStrin…  SubStrin…  Int64     Int64     Int64
─────┼────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
   1 │ NC_000015.10  74343027  g.74343027C>T  snv          heterozygous  C          T                61        58         120
   2 │ NC_000015.10  75400778  g.75400778C>G  snv          heterozygous  C          G               108        79         187
   3 │ NC_000015.10  89327201  g.89327201C>T  snv          heterozygous  C          T               243       241         486
   4 │ NC_000015.10  48767448  g.48767448A>C  snv          heterozygous  A          C                72        70         142
   5 │ NC_000015.10  75411685  g.75411685T>C  snv          heterozygous  T          C                79        81         160
   6 │ NC_000015.10  66703292  g.66703292C>T  snv          heterozygous  C          T                70        60         130
   7 │ NC_000015.10  89325639  g.89325639G>A  snv          heterozygous  G          A               257       267         524
   8 │ NC_000015.10  89330184  g.89330184G>A  snv          heterozygous  G          A               258       287         548
   9 │ NC_000015.10  89330184  g.89330184G>A  snv          heterozygous  G          A               258       287         548
  10 │ NC_000015.10  89325639  g.89325639G>A  snv          heterozygous  G          A               257       267         524
  11 │ NC_000015.10  42401752  g.42401752G>A  snv          homozygous    G          A                61       212         273
  12 │ NC_000015.10  89327201  g.89327201C>T  snv          heterozygous  C          T               243       241         486
  13 │ NC_000015.10  38339896  g.38339896G>A  snv          heterozygous  G          A                56        86         144
  14 │ NC_000015.10  26869324  g.26869324A>T  snv          heterozygous  A          T                62        49         113
  15 │ NC_000015.10  66435145  g.66435145G>A  snv          heterozygous  G          A                98        95         193
  16 │ NC_000015.10  60514655  g.60514655G>A  snv          heterozygous  G          A                94        99         194
  17 │ NC_000015.10  42410947  g.42410947A>G  snv          heterozygous  A          G               153       123         276
  18 │ NC_000015.10  75430368  g.75430368C>T  snv          heterozygous  C          T                80        62         142
  19 │ NC_000015.10  25375494  g.25375494T>C  snv          heterozygous  T          C               103       104         207
  20 │ NC_000015.10  60497497  g.60497497C>A  snv          heterozygous  C          A                61        65         126
  21 │ NC_000015.10  74891539  g.74891539C>T  snv          heterozygous  C          T               118       124         242
  22 │ NC_000015.10  48488433  g.48488433A>G  snv          heterozygous  A          G               367       122         492
  23 │ NC_000015.10  89318565  g.89318565A>G  snv          heterozygous  A          G               303        98         404
  24 │ NC_000015.10  89323426  g.89323426C>G  snv          heterozygous  C          G                93       109         202
  25 │ NC_000015.10  89318595  g.89318595T>C  snv          heterozygous  T          C               321       128         453
  26 │ NC_000015.10  48488437  g.48488437T>C  snv          heterozygous  T          C               356       132         488
CLOSED: [2023-05-01 Mon 17:18]
*** KILL Chromosome1 15 :Test haplotype caller : échec car CIGARE non mis à jour
CLOSED: [2023-05-13 Sat 18:29] SCHEDULED: <2023-05-01 Mon>

[21.47019]

[21.51279]

On confirnme le nombre de SNP:
❯ awk '!/^#/ && $10~/:FN:/ && $10~/SNP/' test-allchr.vcf  | wc -l
6665
Une minorité concerne des problème d'haploides
❯ awk '!/^#/ && $10~/:FN:/ && $11!~/NOCALL/ && $10~/SNP/' test-allchr.vcf
304
avec 1/3 où l'exome manque une allèles
❯ awk '!/^#/ && $10~/:FN:/ && $11!~/NOCALL/ && $10~/SNP/ && $10~/homalt/' test-allchr.vcf  | wc -l
101
et 2/3 où il y a une allèle "en trop"

Replacement in archive/bisonex.org_archive at line 155 [20.46128]

B:BD[21.51280] → [21.51280:51487]

#+begin_src
julia -Jbisonex.so --project=. insertVariants.jl `63003856_S135_chr15.bam` 63003856_S135_chr15_inserted.bam
scp 63003856_S135_chr15_inserted.bam* meso:/Work/Users/apraga/bisonex/tests/synthetic/

[21.51280]

[21.51487]

La majorité ne sont pas vu
❯ awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/' test-allchr.vcf  | wc -l
6361

Insertion in archive/bisonex.org_archive at line 159 [20.46128]

[21.51488]

Nombre de reads pour chaque position en bash (!)
#+begin_src bash
 awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/ {print $1":"$2"-"$2}' test-allchr.vcf  |  xargs -I {} sh -c 'echo -n {}";"; samtools view ../NA12878_NIST.b
am {} | wc -l' > count.csv

Replacement in archive/bisonex.org_archive at line 165 [20.46128]

B:BD[21.51499] → [21.51499:51923]

#+begin_src sh :dir /ssh:meso:/Work/Users/apraga/bisonex/tests/synthetic :results silent
ln -s /Work/Projects/bisonex/data/dbSNP/GRCh38.p13/dbSNP.gz .
ln -s /Work/Projects/bisonex/data/dbSNP/GRCh38.p13/dbSNP.gz.tbi
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.dict .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.fna .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef.fna.fai .

[21.51499]

[21.51923]

* KILL Julia
CLOSED: [2023-03-13 lun. 11:11]
:PROPERTIES:
:ARCHIVE_TIME: 2023-03-13 lun. 15:52
:ARCHIVE_FILE: c:/Users/apraga/org/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Validation : NA12878/GIAB/Exons seuls/D'où vient la différence ?/Statistiques
:ARCHIVE_CATEGORY: GIAB
:ARCHIVE_TODO: KILL
:END:
Conflict BAM et vcf
#+begin_src julia
using GeneticVariation
reader = VCF.Reader(open("../out/test-bed/test-allchr.vcf", "r"))
fn = 0
notSeen = 0
missingAllel = 0
surnumAllel = 0
for record in reader
    global fn, notSeen
    global missingAllel, surnumAllel
    if VCF.genotype(record)[1][2] == "FN" && VCF.genotype(record)[1][5] == "SNP"
        # println(record)
        # println("$(VCF.chrom(record))  $(VCF.pos(record))")
        fn = fn +1
        if VCF.genotype(record)[2][5] == "NOCALL"
            notSeen = notSeen + 1
        else
            if VCF.genotype(record)[1][6] == "homalt"
                missingAllel = missingAllel + 1
            elseif VCF.genotype(record)[2][6] == "homalt"
                surnumAllel = surnumAllel + 1
            end
        end
    end
end
close(reader)
println("SNP: false negative $fn")
println("SNP: not seen $notSeen")
println("SNP: missing allel $missingAllel")
println("SNP: surnumeraries allel $surnumAllel")

Replacement in archive/bisonex.org_archive at line 208 [20.46128]

B:BD[21.51934] → [21.51934:52121]

puis
#+begin_src
gatk --java-options "-Xmx3072M" HaplotypeCaller --input 63003856_S135_chr15_inserted.bam --output testchr15.vcf.gz --reference genomeRef.fna  --tmp-dir . -L NC_000015.10

[21.51934]

[21.52121]

SNP: false negative 6665
SNP: not seen 6361
SNP: missing allel 101
SNP: surnumeraries allel 203
1. On confirme le nombre de SNP.
2. Une minorité concerne des problème d'haploides avec
   - 1/3 où l'exome manque une allèles
   - 2/3 où il y a une allèle "en trop"
3. La majorité ne sont pas vu (6361)
Nombre de reads pour chaque position en bash (!)
#+begin_src bash
 awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/ {print $1":"$2"-"$2}' test-allchr.vcf  |  xargs -I {} sh -c 'echo -n {}";"; samtools view ../NA12878_NIST.b
am {} | wc -l' > count.csv
* KILL Reads en dehors des exons
CLOSED: [2023-03-09 Thu 22:43]
:PROPERTIES:
:ARCHIVE_TIME: 2023-03-13 lun. 15:55
:ARCHIVE_FILE: c:/Users/apraga/org/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Validation : NA12878/GIAB/Exons seuls/D'où vient la différence ?/Statistiques
:ARCHIVE_CATEGORY: GIAB
:ARCHIVE_TODO: KILL
:END:
Ça a l'air sur des exemples simples ...
#+begin_src sh
wget https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.gff.gz
awk '/BestRefSeq\texon/ && /transcript_id=NM/ {print $1"\t"$4"\t"$5;}' GRCh38_latest_genomic.gff | grep ^NC | save exons.csv

Replacement in archive/bisonex.org_archive at line 239 [20.46128]

B:BD[21.52132] → [21.52132:52230]

scp meso:/Work/Users/apraga/bisonex/tests/synthetic/testchr15.vcf.gz haplotypecaller-chr15.vcf.gz

[21.52132]

[21.52230]

#+begin_src julia
using CSV, DataFrames, Intervals

Replacement in archive/bisonex.org_archive at line 242 [20.46128]

B:BD[21.52231] → [21.52231:53198]

Aucun variant inséré
- base quality ok
  -
**** DONE bam out : non appelé
CLOSED: [2023-05-01 Mon 21:57]
gatk --java-options "-Xmx3072M" HaplotypeCaller --input 63003856_S135_chr15_inserted.bam     --output haplotypecaller-chr15.vcf.gz --reference genomeRef.f
na  --tmp-dir . -L NC_000015.10  --bam-output debug.bam
**** DONE --linked-de-bruijn-graph : idem
CLOSED: [2023-05-01 Mon 21:57]
readlink testchr15.vcf.gz -f^C
[apraga@mesointeractive synthetic]$ gatk --java-options "-Xmx3072M" HaplotypeCaller --input 63003856_S135_chr15_inserted.bam     --output haplotypecaller-chr15.vcf.gz --reference genomeRef.fna  --tmp-dir . -L NC_000015.10  --linked-de-bruijn-graph
**** KILL regénérer fastq
CLOSED: [2023-05-13 Sat 18:29]
Non
*** KILL Générer bam données pour tous les chromosomes
CLOSED: [2023-05-13 Sat 18:29]
 timeit julia -Jbisonex.so --project=. insertVariants.jl ~/code/bisonex/out/63003856/preprocessing/63003856_S135.bam 63003856_S135_inserted.bam

[21.52231]

[21.53198]

# Check the number of reads for each false negative (stored in count.csv)
# from hap.py output:
# awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/ {print $1":"$2"-"$2}' test-allchr.vcf  |  xargs -I {} sh -c 'echo -n {}";"; samtools view ../NA12878_NIST.b am {} | wc -l' > count.csv

Replacement in archive/bisonex.org_archive at line 246 [20.46128]

B:BD[21.53199] → [21.53199:53312]

40min 516ms 835µs 405ns
Avertissement:
 [W::bam_hdr_read] EOF marker is absent. The input is probably truncated

[21.53199]

[21.53312]

function groupedCount(fname)
    f = DataFrame(CSV.File(fname, header=false))
    transform!(f, :Column1 => ByRow(x -> string.(split(x, ":"))[1]) => :chrom)
    transform!(f, :Column1 => ByRow(x -> parse(Int64, string.(split(x, "-"))[2])) => :pos)
    select!(f, Not([:Column1]))
    rename!(f, :Column2 => :nb)
    groupby(f, :chrom)
end

Replacement in archive/bisonex.org_archive at line 255 [20.46128]

B:BD[21.53313] → [21.53313:53384]

Inserted.bam et excluded.bam (fichier avant le merge)  ont l'air ok...

[21.53313]

[21.53384]

function groupedExons(fname)
    f = DataFrame(CSV.File(fname, header=["chrom", "start", "end"], delim="\t"))
    transform!(f, [:start, :end] => ByRow((x,y) -> Interval(x, y)) => :interval)
    select!(f, Not([:start, :end]))
    groupby(f, :chrom)
end
# Check is position x is in exons for chromosome chr
function isExon(x, exons, chr)
    # Remove duplicates
    exonsU = unique(exons[chr])
    res = transform(exonsU, :interval => ByRow(z -> x in z) => :check)
    # Result only found interval
    found = res[res.check,:].interval
    isempty(found) ? missing : first(found)
end

Replacement in archive/bisonex.org_archive at line 272 [20.46128]

B:BD[21.53385] → [21.53385:53605]

On réessaie à la main : ça passe
#+begin_src
samtools merge test-all.bam inserted.bam excluded.bam
❯ mv test-all.bam `63003856_S135_inserted.bam` -f
❯ mv test-all.bam.bai `63003856_S135_chr15_inserted.bam.bai` -f

[21.53385]

[21.53605]

reads = groupedCount("../NA12878/happy/count.csv")
exons = groupedExons("exons.csv")
for g in range(1, size(reads)[1])
    local found
    found = transform(reads[g], :pos => ByRow(x -> isExon(x, exons, g)) => :exon)
    readsMissing = found[ismissing.(found.exon), :]
    # print("$(k.chrom):")
    print(g)
    print(": $(size(reads[g])[1]) reads, ")
    println("$(size(readsMissing)[1]) not in exons")
end

Replacement in archive/bisonex.org_archive at line 285 [20.46128]

B:BD[21.53615] → [21.53615:53748]

*** DONE BAm2fastq pour avoir CIGAR à jour : échec (variants "cachés")
CLOSED: [2023-05-04 Thu 20:30] SCHEDULED: <2023-05-01 Mon>

[21.53615]

[21.53748]

1: 448 reads, 64 not in exons
2: 307 reads, 47 not in exons
3: 228 reads, 37 not in exons
4: 175 reads, 28 not in exons
5: 237 reads, 38 not in exons
6: 1223 reads, 304 not in exons
7: 274 reads, 52 not in exons
8: 414 reads, 41 not in exons
9: 161 reads, 47 not in exons
10: 194 reads, 37 not in exons
11: 304 reads, 39 not in exons
12: 254 reads, 32 not in exons
13: 168 reads, 120 not in exons
14: 184 reads, 26 not in exons
15: 250 reads, 90 not in exons
16: 239 reads, 29 not in exons
17: 373 reads, 35 not in exons
18: 85 reads, 17 not in exons
19: 576 reads, 46 not in exons
20: 83 reads, 22 not in exons
21: 67 reads, 14 not in exons
22: 117 reads, 24 not in exons

Replacement in archive/bisonex.org_archive at line 309 [20.46128]

B:BD[21.53749] → [21.53749:54036]

On lance la génération de bam depuis le mesocentro (la copie plante via le VPN)
#+begin_src sh
cd /Work/Users/apraga/recherche/bisonex/generate
julia --project=. insertVariants.jl  ../../../bisonex/out/63003856_S135/preprocessing/applybqsr/63003856_S135.bam 63003856_S135_inserted.bam

[21.53749]

[21.54036]

* KILL Répartition par chromosome: variable mais seul le 6 = hotspot
CLOSED: [2023-03-07 Tue 22:44]
:PROPERTIES:
:ARCHIVE_TIME: 2023-03-13 lun. 15:55
:ARCHIVE_FILE: c:/Users/apraga/org/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Validation : NA12878/GIAB/Exons seuls/D'où vient la différence ?/Statistiques
:ARCHIVE_CATEGORY: GIAB
:ARCHIVE_TODO: KILL
:END:
#+begin_src julia
using CSV, DataFrames
f = DataFrame(CSV.File("count.csv", header=false))
size(f[f.Column2 .< 10,:])

Replacement in archive/bisonex.org_archive at line 323 [20.46128]

B:BD[21.54046] → [21.54046:54371]

Workflow après avec désactivé storeDir pour SAMTOOLS_BAM2FQ dans nextflow.config (pourquoi ??)
#+begin_src nextflow
include { SAMTOOLS_BAM2FQ }                            from "${params.modulesDir}/samtools/bam2fq/main"
include { SAMTOOLS_SORT as sortBamByName }             from "${params.modulesDir}/samtools/sort/main"

[21.54046]

[21.54371]

(4430, 2)
#+begin_src julia
using CSV, DataFrames

Replacement in archive/bisonex.org_archive at line 329 [20.46128]

B:BD[21.54372] → [21.54372:54667]

workflow {
    f = Channel.fromPath("${params.dataDir}/synthetic/63003856_S135_inserted.bam",
                         checkIfExists: true).map{it -> [["id": "synthetic_63003856"], it]}
    // Important: use "-n" option !!
    sortBamByName(f)
    SAMTOOLS_BAM2FQ(sortBamByName.out.bam, true)
}

[21.54372]

[21.54667]

function cleanCount(fname)
    f = DataFrame(CSV.File(fname, header=false))
    transform!(f, :Column1 => ByRow(x -> string.(split(x, ":"))[1]) => :chrom)
    transform!(f, :Column1 => ByRow(x -> string.(split(x, "-"))[2]) => :pos)
    select!(f, Not([:Column1]))
    rename!(f, :Column2 => :nb)
end
f = cleanCount("count.csv")
grouped = groupby(f, :chrom)
for (k, g) in pairs(grouped)
    println("$(k.chrom): $(size(g, 1))")
end

Replacement in archive/bisonex.org_archive at line 343 [20.46128]

B:BD[21.54677] → [21.54677:54781]

Puis
#+begin_src
cp work/34/fb2fc136f6f6d7f42d0960512f06de/*.fq.gz /Work/Groups/bisonex/data/synthetic/

[21.54677]

[21.54781]


#+RESULTS:
: NC_000001.11: 448
: NC_000002.12: 307
: NC_000003.12: 228
: NC_000004.12: 175
: NC_000005.10: 237
: NC_000006.12: 1223
: NC_000007.14: 274
: NC_000008.11: 414
: NC_000009.12: 161
: NC_000010.11: 194
: NC_000011.10: 304
: NC_000012.12: 254
: NC_000013.11: 168
: NC_000014.9: 184
: NC_000015.10: 250
: NC_000016.10: 239
: NC_000017.11: 373
: NC_000018.10: 85
: NC_000019.10: 576
: NC_000020.11: 83
: NC_000021.9: 67
: NC_000022.11: 117
* KILL Awk
CLOSED: [2023-03-12 Sun 22:12]
:PROPERTIES:
:ARCHIVE_TIME: 2023-03-13 lun. 15:55
:ARCHIVE_FILE: c:/Users/apraga/org/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Validation : NA12878/GIAB/Exons seuls/D'où vient la différence ?/Statistiques
:ARCHIVE_CATEGORY: GIAB
:ARCHIVE_TODO: KILL
:END:
NB: awk car bcftools query ne semble pas prendre en compte les nouvelles colonnes
On confirnme le nombre de SNP:
❯ awk '!/^#/ && $10~/:FN:/ && $10~/SNP/' test-allchr.vcf  | wc -l
6665
Une minorité concerne des problème d'haploides
❯ awk '!/^#/ && $10~/:FN:/ && $11!~/NOCALL/ && $10~/SNP/' test-allchr.vcf
304
avec 1/3 où l'exome manque une allèles
❯ awk '!/^#/ && $10~/:FN:/ && $11!~/NOCALL/ && $10~/SNP/ && $10~/homalt/' test-allchr.vcf  | wc -l
101
et 2/3 où il y a une allèle "en trop"
La majorité ne sont pas vu
❯ awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/' test-allchr.vcf  | wc -l
6361
Nombre de reads pour chaque position en bash (!)
#+begin_src bash
 awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/ {print $1":"$2"-"$2}' test-allchr.vcf  |  xargs -I {} sh -c 'echo -n {}";"; samtools view ../NA12878_NIST.b
am {} | wc -l' > count.csv

Deletion in archive/bisonex.org_archive at line 402 [20.46128]

B:BD[21.54791] → [21.54791:55086]

*** KILL Lancer pipeline
CLOSED: [2023-05-04 Thu 20:30] SCHEDULED: <2023-05-01 Mon>
NXF_OPTS=-D"user.name=apraga" nextflow run   main.nf -c nextflow.config  -profile standard,helios -bg --input="/Work/Groups/bisonex/data/synthetic/synthetic_63003856_{1,2}.fq.gz" --outdir out/synthetic_63003856

Replacement in archive/bisonex.org_archive at line 403 [20.46128]

B:BD[22.51043] → [22.51043:51074]

* Amélioration :amelioration:

[22.51043]

[22.51074]

* KILL Comprendre/améliorer Recall SNP 0.855
CLOSED: [2023-03-13 lun. 15:55] SCHEDULED: <2023-03-04 Sat>

Replacement in archive/bisonex.org_archive at line 406 [20.46128]

B:BD[22.51087] → [22.51087:51202]

:ARCHIVE_TIME: 2023-09-10 Sun 16:45
:ARCHIVE_FILE: ~/roam/personal/projects/bisonex.org
:ARCHIVE_CATEGORY: bisonex

[22.51087]

[22.51202]

:ARCHIVE_TIME: 2023-03-13 lun. 15:55
:ARCHIVE_FILE: c:/Users/apraga/org/projects/bisonex.org
:ARCHIVE_OLPATH: Tests/Validation : NA12878/GIAB/Exons seuls/D'où vient la différence ?/Statistiques
:ARCHIVE_CATEGORY: GIAB
:ARCHIVE_TODO: KILL

Insertion in archive/bisonex.org_archive at line 412 [20.46128]

[22.51208]

 on est inférieur à Kumaran et al 2019
** KILL Regarder les FN (SNP)
CLOSED: [2023-03-13 lun. 15:55] SCHEDULED: <2023-03-04 Sat  >
*** Manuel:
NC_000001.11:1385919 pas de read 1/1:FN:.:i1_5:INDEL:homalt:.
NC_000001.11:1623412 1 read     1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1668449 33 read sur 160 voient l'allèle alternative 1/1:FN:am:ti:SNP:homalt:.
NC_000001.11:1676135 67 reads, non vu 0/1:FN:.:ti:SNP:het:.
NC_000001.11:1734812 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1745808 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1745814 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1953616 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:2512975 0/1:FN:.:ti:SNP:het:

File move: bisonex.org → bisonex.org
BF:BFD[5.13] → [5.37662:37697]
BF:BF[5.37697] → [5.35:35]
[4.15272215]
[5.35]

Cleaning up lists and projects

Dependencies

In channels

Change contents

File deletion: projects

File deletion: art-capture-1.png

File deletion: check-snv-chr15.png

File deletion: art-exon6-offset1000.png

File deletion: insertion-demo.png

File deletion: simuscop-success.png

File deletion: illumina-ref-exon6.png

File deletion: test-intersect-chr15.png

File deletion: simuscop-200-chr1-1.png

File deletion: haplotype-missing-2.png

File deletion: test-nointersect-chr15.png

File deletion: simuscop-error.png

File deletion: .hypb

File deletion: simuscop-200-chr1-2.png

File deletion: haplotype-missing.png

File deletion: reads.png