#!/bin/bash -Ceuo pipefail
mkdir -p HCC1395BL_c_01_gDNA_0001_A237FLHLT3_2/
cnv_pipe calc-panel-coverage \
        HCC1395BL_c_01_gDNA_0001_A237FLHLT3_2.recalibrated.bam \
        altera_v3_panel.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/HCC1395BL_c_01_gDNA_0001_A237FLHLT3_2_counts.tsv \
        4 \
        20 \
        $(pwd)/HCC1395BL_c_01_gDNA_0001_A237FLHLT3_2/