#!/bin/bash -Ceuo pipefail
mkdir -p 1029_BRTT-N1-BDNA-1_2375WFLT3_s50/
cnv_pipe calc-panel-coverage \
        1029_BRTT-N1-BDNA-1_2375WFLT3_s50.recalibrated.bam \
        altera_v3_panel.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/1029_BRTT-N1-BDNA-1_2375WFLT3_s50_counts.tsv \
        4 \
        20 \
        $(pwd)/1029_BRTT-N1-BDNA-1_2375WFLT3_s50/