.command.sh - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP (Sig_18_Blood;Sig_18_Blood)

File Info

Filename: .command.sh
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/937932147aec8e0af7714df84458b1/.command.sh
Size: 513 bytes
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:VCF_ANNOTATE_INDEL_ENTROPY:SAMTOOLS_MPILEUP (Sig_18_Blood;Sig_18_Blood)
Attempt

Content

#!/bin/bash -Ceuo pipefail
samtools mpileup \
    --fasta-ref Homo_sapiens_assembly38.fasta \
    --output Sig_18_Blood.mpileup \
    -A -B -Q 0 \
    -l Sig_18_Blood.bed \
    Sig_18_Blood.recalibrated.bam
bgzip Sig_18_Blood.mpileup

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL: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