.command.sh - Workdir - 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)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/21e50443944e3ff158de73ae75ee62/.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

#!/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