#!/bin/bash -Ceuo pipefail
bcftools concat \
--output HCC1395_tumor_vs_HCC1395_BL.snv_indel.merged.vcf.gz \
--allow-overlaps --output-type z --write-index=tbi \
--threads 6 \
HCC1395_tumor_vs_HCC1395_BL.snv_indel.tnseq.snv.vcf.gz HCC1395_tumor_vs_HCC1395_BL.snv_indel.strelka.indel.vcf.gz
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:VCF_SOMATIC_SNV_INDEL:BCFTOOLS_CONCAT":
bcftools: $(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*$//')
END_VERSIONS