#!/bin/bash -Ceuo pipefail
bcftools index HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_RPM.vcf.gz

bcftools \
    annotate \
    --output-type z --write-index=tbi -c CHROM,FROM,TO,BlacklistRegion \
    --annotations blacklist_grch38.bed.gz \
    --header-lines blacklist_header.txt \
    --output HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_BL.vcf.gz \
    --threads 1 \
    HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_indels_RPM.vcf.gz

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_BLACKLIST:BCFTOOLS_ANNOTATE":
    bcftools: $( bcftools --version |& sed '1!d; s/^.*bcftools //' )
END_VERSIONS