File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/e8a0a53bb3ec7ec21fdf0b3d90038c/.command.sh
Size
634 bytes
Task
DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER:SENTIEON_HAPLOTYPER (germline_control_1;chr4_30730753-30730788.bed)
Attempt

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#!/bin/bash -Ceuo pipefail
sentieon driver \
     \
    -r Homo_sapiens_assembly38.fasta \
    -t 12 \
    --interval chr4_30730753-30730788.bed.gz \
    -i HCC1395_BL.recalibrated.bam \
     \
    --algo Haplotyper -d dbsnp_146.hg38.vcf.gz  --emit_mode variant germline_control_1.haplotyper.chr4_30730753-30730788.bed.unfiltered.vcf.gz \


cat <<-END_VERSIONS > versions.yml
"DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC: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