#!/bin/bash -Ceuo pipefail
vep \
    -i HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff.ann.vcf.gz \
    -o HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff_VEP.ann.vcf.gz \
    --stats_file HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_custom.ann_snpEff_VEP.ann.summary.html      --vcf  --everything --filter_common --per_gene --total_length --offline --format vcf \
    --compress_output bgzip \
     \
    --assembly GRCh38 \
    --species homo_sapiens \
    --cache \
    --cache_version 113 \
    --dir_cache ${PWD}/113_GRCh38 \
    --fork 4


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