#!/bin/bash -Ceuo pipefail
gatk --java-options "-Xmx3276M -XX:-UsePerfData" \
    MergeVcfs \
    --INPUT HCC1395_tumor_vs_HCC1395_BL.strelka.chr21_44102678-44103072.bed.somatic_snvs.vcf.gz --INPUT HCC1395_tumor_vs_HCC1395_BL.strelka.chr21_5117003-5117331.bed.somatic_snvs.vcf.gz --INPUT HCC1395_tumor_vs_HCC1395_BL.strelka.chr21_34799195-34799564.bed.somatic_snvs.vcf.gz \
    --OUTPUT HCC1395_tumor_vs_HCC1395_BL.strelka.somatic_snvs.vcf.gz \
    --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict \
    --TMP_DIR . \


cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_STRELKA:MERGE_STRELKA_SNVS":
    gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*$//')
END_VERSIONS