File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/c9bd1940495138659c37c221c762b5/.command.sh
Size
632 bytes
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER (Sig_18_Blood;chr21_5117103-5117231.bed)
Attempt

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#!/bin/bash -Ceuo pipefail
sentieon driver \
     \
    -r Homo_sapiens_assembly38.fasta \
    -t 12 \
    --interval chr21_5117103-5117231.bed.gz \
    -i Sig_18_Blood.recalibrated.bam \
     \
    --algo Haplotyper -d dbsnp_146.hg38.vcf.gz  --emit_mode variant Sig_18_Blood.haplotyper.chr21_5117103-5117231.bed.unfiltered.vcf.gz \


cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER":
    sentieon: $(echo $(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS