#!/bin/bash -Ceuo pipefail
snv=$(bcftools view -s 'HCC1395_BL' -f PASS negative_somatic_control_1.snv_indel.phased.vep.final.vcf.gz | bcftools view -H -e 'FORMAT/AF[0:0]<0.05' -v snps   | wc -l)
indel=$(bcftools view -s 'HCC1395_BL' -f PASS negative_somatic_control_1.snv_indel.phased.vep.final.vcf.gz | bcftools view -H -e 'FORMAT/AF[0:0]<0.05' -v indels | wc -l)

{
    printf "snv_count\t%s\n"   "$snv"
    printf "indel_count\t%s\n" "$indel"
} > negative_somatic_control_1.snv_indel.tsv

cat <<-END_VERSIONS > versions.yml
"DAQ:CONTROL_METRICS:NEGATIVE_SOMATIC_METRICS:NEGATIVE_SOMATIC_SNV_INDEL":
    bcftools: $(bcftools --version | head -n1 | awk '{print $2}')
END_VERSIONS