#!/bin/bash -Ceuo pipefail
mkdir -p NA12878_c_0003_gDNA_0002_A23WF23LT4_1/
cnv_pipe calc-panel-coverage \
        NA12878_c_0003_gDNA_0002_A23WF23LT4_1.recalibrated.bam \
        altera_v3_panel.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/NA12878_c_0003_gDNA_0002_A23WF23LT4_1_counts.tsv \
        4 \
        20 \
        $(pwd)/NA12878_c_0003_gDNA_0002_A23WF23LT4_1/