File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/022a129fb8629e8648544de7c9c06e/.command.sh
Size
588 bytes
Task
DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_FORCECALL (germline_control_2;germline_rescue_targets)
Attempt

Content

View in new tab 
#!/bin/bash -Ceuo pipefail
sentieon driver \
     \
    -r Homo_sapiens_assembly38.fasta \
    -t 12 \
    --interval germline_rescue_targets.bed \
    -i Sig_18_Blood.recalibrated.bam \
     \
    --algo Haplotyper --given germline_control_2.dv_only_sites.vcf.gz  --emit_mode variant germline_control_2.forcecall.unfiltered.vcf.gz \


cat <<-END_VERSIONS > versions.yml
"DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_FORCECALL":
    sentieon: $(echo $(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS