#!/bin/bash -Ceuo pipefail
sentieon driver -t 31 -i HCC1395_tumor.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector  --fun score_info HCC1395_tumor.md.score

sentieon driver -t 31 -i HCC1395_tumor.bam -r Homo_sapiens_assembly38.fasta --algo Dedup  --score_info HCC1395_tumor.md.score --metrics HCC1395_tumor.md.metrics HCC1395_tumor.md.bam

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