#!/bin/bash -Ceuo pipefail
tabix positive_somatic_control_2.snv_indel.whatshap.chr5.phased.vcf.gz
tabix positive_somatic_control_2.snv_indel.whatshap.chr21.phased.vcf.gz

bcftools concat \
    --output positive_somatic_control_2.snv_indel.phased.vcf.gz \
    --allow-overlaps --output-type z --write-index=tbi \
    --threads 1 \
    positive_somatic_control_2.snv_indel.whatshap.chr5.phased.vcf.gz positive_somatic_control_2.snv_indel.whatshap.chr21.phased.vcf.gz

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