#!/bin/bash -Ceuo pipefail
vep \
    -i HCC1395_tumor_vs_HCC1395_BL.snv_indel.phased.vcf.gz \
    -o HCC1395_tumor_vs_HCC1395_BL.snv_indel.phased.vep.vcf.gz \
    --stats_file HCC1395_tumor_vs_HCC1395_BL.snv_indel.phased.vep.summary.html --vcf --offline --flag_pick --canonical --hgvs --format vcf \
    --compress_output bgzip \
    --fasta Homo_sapiens_assembly38.fasta \
    --assembly GRCh38 \
    --species homo_sapiens \
    --cache \
    --cache_version 113 \
    --dir_cache ${PWD}/113_GRCh38 \
    --fork 4


cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:VCF_SOMATIC_SNV_INDEL:ENSEMBLVEP_VEP":
    ensemblvep: $( echo $(vep --help 2>&1) | sed 's/^.*Versions:.*ensembl-vep : //;s/ .*$//')
END_VERSIONS