#!/bin/bash -Ceuo pipefail
bcftools index HCC1395_BL.deconflicted_germline.vcf.gz
bcftools \
annotate \
--output-type z --write-index=tbi -c CHROM,FROM,TO,RPMCat \
--annotations repeatmasker_grch38.bed.gz \
--header-lines repeatmasker_header.txt \
--output HCC1395_BL.deconflicted_germline_RPM.vcf.gz \
--threads 1 \
HCC1395_BL.deconflicted_germline.vcf.gz
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_REPEATMASKER:BCFTOOLS_ANNOTATE":
bcftools: $( bcftools --version |& sed '1!d; s/^.*bcftools //' )
END_VERSIONS