#!/bin/bash -Ceuo pipefail
gatk --java-options "-Xmx3276M -XX:-UsePerfData" \
    MergeVcfs \
    --INPUT germline_control_1.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz --INPUT germline_control_1.haplotyper.chr14_64122012-64122133.bed.unfiltered.vcf.gz --INPUT germline_control_1.haplotyper.chr1_69091-70008.bed.unfiltered.vcf.gz --INPUT germline_control_1.haplotyper.chr4_30730753-30730788.bed.unfiltered.vcf.gz --INPUT germline_control_1.haplotyper.chr8_93795409-93795507.bed.unfiltered.vcf.gz \
    --OUTPUT germline_control_1.haplotyper.unfiltered.vcf.gz \
    --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict \
    --TMP_DIR . \


cat <<-END_VERSIONS > versions.yml
"DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS":
    gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*$//')
END_VERSIONS