#!/bin/bash -Ceuo pipefail
msisensor2 msi \
-b 2 \
\
\
-d 1500_dropped_panel_with_boosted_msi_regions.tsv \
-e xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed \
-t Sig_18_Blood.recalibrated.bam \
-n reference-NA12878-downsampled-500k.bam \
-o negative_somatic_control_2_xgen
cat <<-END_VERSIONS > versions.yml
"DAQ:CONTROL_VARIANT_CALLING:CONTROL_SOMATIC_VC:MSISENSOR2_MSI":
msisensor2: $(echo $(msisensor2 2> >(grep Version) | sed 's/Version: v//g'))
END_VERSIONS