File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/dd1f4ef651f78645bbfd207daf2b32/.command.sh
Size
633 bytes
Task
DAQ:SENTIEON_BQSR:QUALCAL_TABLE (1136_3LU-T1-TDNA-1_A23MHWWLT4_1)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
sentieon driver \
    -t 31 \
    -r Homo_sapiens_assembly38.fasta \
    -i 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam \
    --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed \
    --algo QualCal \
     \
    -k dbsnp_146.hg38.vcf.gz -k Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -k Homo_sapiens_assembly38.known_indels.vcf.gz \
    1136_3LU-T1-TDNA-1_A23MHWWLT4_1.table

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