#!/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 HCC1395_tumor.recalibrated.bam \
    -n reference-NA12878-downsampled-500k.bam \
    -o positive_somatic_control_1_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