#!/bin/bash -Ceuo pipefail
sentieon driver \
     \
    -r Homo_sapiens_assembly38.fasta \
    -t 12 \
    --interval germline_rescue_targets.bed \
    -i Sig_18_Blood.recalibrated.bam \
     \
    --algo Haplotyper --given Sig_18_Blood.dv_only_sites.vcf.gz  --emit_mode variant Sig_18_Blood.forcecall.unfiltered.vcf.gz \


cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_FORCECALL":
    sentieon: $(echo $(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS