File Info

Filename
.command.sh
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/36cd4bbf0af9a0e1fb0b57ddc578ba/.command.sh
Size
525 bytes
Task
DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP (germline_control_1;germline_control_1)
Attempt

Content

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#!/bin/bash -Ceuo pipefail
samtools mpileup \
    --fasta-ref Homo_sapiens_assembly38.fasta \
    --output germline_control_1.mpileup \
    -A -B -Q 0 \
    -l germline_control_1.bed \
    HCC1395_BL.recalibrated.bam
bgzip germline_control_1.mpileup

cat <<-END_VERSIONS > versions.yml
"DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP":
    samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
END_VERSIONS