#!/bin/bash -Ceuo pipefail
bcftools index Sig_18_Blood.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 Sig_18_Blood.deconflicted_germline_RPM.vcf.gz \
    --threads 1 \
    Sig_18_Blood.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