#!/bin/bash -Ceuo pipefail
mkdir -p HG03401_c_0001_gDNA_0001_B23H2H2LT4_3/
cnv_pipe calc-panel-coverage \
        HG03401_c_0001_gDNA_0001_B23H2H2LT4_3.recalibrated.bam \
        altera_v3_panel.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/HG03401_c_0001_gDNA_0001_B23H2H2LT4_3_counts.tsv \
        4 \
        20 \
        $(pwd)/HG03401_c_0001_gDNA_0001_B23H2H2LT4_3/