File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/58ee5f1d13c2869d96d8f491b73143/.command.sh
Size
681 bytes
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:MERGE_SENTIEON_HAPLOTYPER_VCFS (Sig_18_Blood)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
gatk --java-options "-Xmx3276M -XX:-UsePerfData" \
    MergeVcfs \
    --INPUT Sig_18_Blood.haplotyper.chr21_44120631-44120778.bed.unfiltered.vcf.gz --INPUT Sig_18_Blood.haplotyper.chr21_5117103-5117231.bed.unfiltered.vcf.gz \
    --OUTPUT Sig_18_Blood.haplotyper.unfiltered.vcf.gz \
    --SEQUENCE_DICTIONARY Homo_sapiens_assembly38.dict \
    --TMP_DIR . \


cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL: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