fcliquet

#!/bin/bash

# Normalize VCF first if not already done !
# this annotation command will copy all the INFO fields from the gnomAD bcf to your VCF

bcftools annotate -a /pasteur/helix/projects/ghfc_wgs/references/GRCh38/gnomAD/gnomad_v4.1_allChroms.bcf --threads 12 -c INFO -O z -o my_vcf.gnomad.vcf.gz my_vcf.norm.vcf.gz

fcliquet

cache 1
dir_cache  '/pasteur/helix/projects/ghfc_wgs/references/ensembl-vep-data'
assembly 'GRCh38'
species 'homo_sapiens'
fasta '/pasteur/helix/projects/ghfc_wgs/references/GRCh38/chr/hs38DH.fa'
offline 1
force_overwrite 1
buffer_size '500'
db_version '112'
gencode_basic 1

fcliquet

#!/bin/bash

#SBATCH --job-name=job_name
#SBATCH --partition=ghfc
#SBATCH --qos=ghfc
#SBATCH --ntasks=1
#SBATCH --mem=4G
#SBATCH --cpus-per-task=1

# exit when any command fails