#!/bin/bash -Ceuo pipefail
samtools mpileup \
    --fasta-ref Homo_sapiens_assembly38.fasta \
    --output germline_control_2.mpileup \
    -A -B -Q 0 \
    -l germline_control_2.bed \
    Sig_18_Blood.recalibrated.bam
bgzip germline_control_2.mpileup

cat <<-END_VERSIONS > versions.yml
"DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP":
    samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
END_VERSIONS