#!/bin/bash -Ceuo pipefail
bcftools concat \
    --output positive_somatic_control_1.snv_indel.merged.vcf.gz \
    --allow-overlaps --output-type z --write-index=tbi \
    --threads 1 \
    positive_somatic_control_1.snv_indel.tnseq.snv.vcf.gz positive_somatic_control_1.snv_indel.strelka.indel.vcf.gz

cat <<-END_VERSIONS > versions.yml
"DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:VCF_SOMATIC_SNV_INDEL:BCFTOOLS_CONCAT":
    bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
END_VERSIONS