#!/bin/bash -Ceuo pipefail
echo "$(pwd)"
mkdir  -p 3619658685_r13/
cnv_pipe calc-panel-coverage \
        3619658685_r13.bam \
        Renasight_CNV.mosatic.tm.bed \
        $(pwd)/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz \
        $(pwd)/counts.tsv \
        1 \
        20 \
        $(pwd)/3619658685_r13/ \