#!/bin/bash -Ceuo pipefail
bcftools index HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_BL.vcf.gz
bcftools \
annotate \
--output-type z --write-index=tbi -c CHROM,FROM,TO,LowDepthRegion,LowDepthReads,LowDepthPct \
--annotations low_depth_grch38.tsv.gz \
--header-lines low_depth_header.txt \
--output HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_custom.ann.vcf.gz \
--threads 1 \
HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs_BL.vcf.gz
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_LOWDEPTH:BCFTOOLS_ANNOTATE":
bcftools: $( bcftools --version |& sed '1!d; s/^.*bcftools //' )
END_VERSIONS