#!/bin/bash -Ceuo pipefail
gatk --java-options "-Xmx3276M -XX:-UsePerfData" \
    MergeVcfs \
    --INPUT pos_somatic_015.strelka.chr1_68991-70108.bed.somatic_indels.vcf.gz --INPUT pos_somatic_015.strelka.chr9_110971973-110972217.bed.somatic_indels.vcf.gz --INPUT pos_somatic_015.strelka.chr19_15162349-15162662.bed.somatic_indels.vcf.gz --INPUT pos_somatic_015.strelka.chr10_74133927-74134264.bed.somatic_indels.vcf.gz --INPUT pos_somatic_015.strelka.chr4_22420786-22421189.bed.somatic_indels.vcf.gz --INPUT pos_somatic_015.strelka.chr16_25246607-25247490.bed.somatic_indels.vcf.gz --INPUT pos_somatic_015.strelka.chr20_14085521-14085828.bed.somatic_indels.vcf.gz --INPUT pos_somatic_015.strelka.chr6_138229684-138229952.bed.somatic_indels.vcf.gz --INPUT pos_somatic_015.strelka.chr12_102480219-102480663.bed.somatic_indels.vcf.gz \
    --OUTPUT pos_somatic_015.strelka.somatic_indels.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_INDELS":
    gatk4: $(echo $(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*$//')
END_VERSIONS