#!/bin/bash -Ceuo pipefail
sentieon driver -r Homo_sapiens_assembly38.fasta \
\
--algo TNfilter \
--tumor_sample 1029_16G-T1-TDNA-1_B23KFCWLT4_1 --normal_sample 1029_16G-N1-BDNA-1_B23KGCJLT4_1 --max_event_count 5 \
-v 1029_16G.tnseq.vcf.gz \
--contamination 1029_16G.tnseq.contamination_data.tsv \
--tumor_segments 1029_16G.tnseq.segments \
--orientation_priors 1029_16G.tnseq.orientation_data.tsv \
1029_16G.tnseq.filtered.vcf.gz
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TNSEQ:SENTIEON_TNFILTER":
sentieon: $(echo $(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g")
END_VERSIONS