#!/bin/bash -Ceuo pipefail
sentieon driver \
    -t 12 \
    -r Homo_sapiens_assembly38.fasta \
     \
    -i Sig_18_Blood.recalibrated.bam -i Sig_18_tissue.recalibrated.bam \
    --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_chr21_padded100bp.bed \
    --algo TNhaplotyper2 \
    --tumor_sample Sig_18_tissue --normal_sample Sig_18_Blood \
    --call_germline_sites \
    --germline_vcf af-only-gnomad.hg38.vcf.gz \
    --pon pon_tnseq_42_curated_v4.vcf.gz \
    custom_Sig_18_tumor_normal.tnseq.vcf.gz \
    --algo OrientationBias --tumor_sample Sig_18_tissue custom_Sig_18_tumor_normal.tnseq.orientation_data.tsv \
    --algo ContaminationModel --tumor_sample Sig_18_tissue --normal_sample Sig_18_Blood --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments custom_Sig_18_tumor_normal.tnseq.segments custom_Sig_18_tumor_normal.tnseq.contamination_data.tsv

cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNHAPLOTYPER2":
    sentieon: $(echo $(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS