apraga/org - Change DJY2XLQPXOGPDJHJVQQDYJHPN5HQJ77UKDOBBBVYVPSPF4ZPUP7AC

Bisonex : echec hap.py

Created by Alexis Praga on February 6, 2023

DJY2XLQPXOGPDJHJVQQDYJHPN5HQJ77UKDOBBBVYVPSPF4ZPUP7AC

Dependencies

In channels

main

Change contents

Deletion in projects/bisonex.org at line 2719 [5.35]

∅:D[3.799] → [4.448:449]

B:BD[4.448] → [4.448:449]

B:BD[4.449] → [2.2170:2198]

∅:D[2.2198] → [3.800:1296]

B:BD[4.623] → [3.800:1296]

B:BD[3.1296] → [2.2199:2209]

∅:D[2.2209] → [3.1296:1297]

B:BD[3.1296] → [3.1296:1297]

B:BD[3.1297] → [2.2210:3078]


Télécharger :
#+begin_src
wget       https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/latest/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.bed
wget       https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/latest/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz
wget       https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/latest/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz.tbi
wget https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/latest/md5.in
md5sum ok
#+end_src
Renommer chromosomes sur BED
#+begin_src
sed -i.bak \
-e 's/chr1/NC_000001.11/' \
-e 's/chr2/NC_000002.12/' \
-e 's/chr3/NC_000003.12/' \
-e 's/chr4/NC_000004.12/' \
-e 's/chr5/NC_000005.10/' \
-e 's/chr6/NC_000006.12/' \
-e 's/chr7/NC_000007.14/' \
-e 's/chr8/NC_000008.11/' \
-e 's/chr9/NC_000009.12/' \
-e 's/chr10/NC_000010.11/' \
-e 's/chr11/NC_000011.10/' \
-e 's/chr12/NC_000012.12/' \
-e 's/chr13/NC_000013.11/' \
-e 's/chr14/NC_000014.9/' \
-e 's/chr15/NC_000015.10/' \
-e 's/chr16/NC_000016.10/' \
-e 's/chr17/NC_000017.11/' \
-e 's/chr18/NC_000018.10/' \
-e 's/chr19/NC_000019.10/' \
-e 's/chr20/NC_000020.11/' \
-e 's/chr21/NC_000021.9/' \
-e 's/chr22/NC_000022.11/' \
-e 's/chrX/NC_000023.11/' \
-e 's/chrY/NC_000024.10/' \
-e 's/chrMT/NC_012920.1/' /Work/Groups/bisonex/NA12878/HG001_GRCh38_1_22_v4.2.1_benchmark.bed \
#+end_src
et sur vcf
#+begin_src

Deletion in projects/bisonex.org at line 2720 [5.35]

B:BD[2.3079] → [2.3079:3250]

awk '{print "chr"$2" "$1}' /Work/Groups/bisonex/data/genome/GRCh38.p13/chromosome_mapping.txt > /Work/Groups/bisonex/data/genome/GRCh38.p13/chromosome_mapping_reverse.txt

Deletion in projects/bisonex.org at line 2721 [5.35]

B:BD[2.3251] → [2.3251:3524]

bcftools annotate --rename-chrs /Work/Groups/bisonex/data/genome/GRCh38.p13/chromosome_mapping_reverse.txt /Work/Groups/bisonex/NA12878/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz  -o /Work/Groups/bisonex/NA12878/HG001_GRCh38_1_22_v4.2.1_benchmark_renam
ed.vcf.gz
#+end_src

Insertion in projects/bisonex.org at line 2725 [5.35]

[2.3835]

[6.96992]

na1878.slurm
#+begin_src slurm
#!/bin/bash
#SBATCH -c 4
#SBATCH -p smp
#SBATCH --time=01:00:00
#SBATCH --mem=32G
module load nix/2.11.0
export HGREF=/Work/Groups/bisonex/data-alexis-reference/genome/GRCh38_latest_genomic.fna
dir=/Work/Groups/bisonex/data/NA12878/GRCh38
hap.py ${dir}/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz script/files/vcf/NA12878_NIST7035.vcf -f ${dir}/HG001_GRCh38_1_22_v4.2.1_benchmark.bed -o test
#+end_src
*** DONE Test 1 : vep annot : exécrable
CLOSED: [2023-02-06 lun. 13:40]
INDEL    ALL       276768       274    276494         1500       257        968     26     15       0.000990          0.516917        0.645333         0.001976                     NaN                     NaN                   1.483361                   6.129187
INDEL   PASS       276768       274    276494         1500       257        968     26     15       0.000990          0.516917        0.645333         0.001976                     NaN                     NaN                   1.483361                   6.129187
  SNP    ALL      1937706      1193   1936513         3338       106       2037     11      2       0.000616          0.918524        0.610246         0.001231                  2.0785                1.861183                   1.539064                   2.703663
  SNP   PASS      1937706      1193   1936513         3338       106       2037     11      2       0.000616          0.918524        0.610246         0.001231                  2.0785                1.861183                   1.539064                   2.703663
*** Test 2 sans filtre vep
*** Test 3 : a