.command.sh - Workdir - DAQ:BAM_POSTDEDUP_QC:SENTIEON_HSMETRICS (1136_4Z5-T1-TDNA-1_A23MHWWLT4_1)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/84/4b7b4f34554f1d306dbe5afbc55332/.command.sh
Size: 775 bytes
Task: DAQ:BAM_POSTDEDUP_QC:SENTIEON_HSMETRICS (1136_4Z5-T1-TDNA-1_A23MHWWLT4_1)
Attempt

Content

#!/bin/bash -Ceuo pipefail
sentieon driver \
    -t 31 \
    -r Homo_sapiens_assembly38.fasta \
    -i 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.md.bam \
     \
    --algo HsMetricAlgo \
    --targets_list targets/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed \
    --baits_list baits/xgen-exome-hyb-panel-v2_AND_altera_v3_probes_short_hg38_AND_cdx_spike_custom30off4x_hg38_AND_foresight_clarity.bed \
    1136_4Z5-T1-TDNA-1_A23MHWWLT4_1_xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.sentieon.hs_metrics

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