Target Counts and B-allele Counts

The target counting stage and its output are the same for the germline CNV calling case. The target intervals with the read counts are output in a *.target.counts file. The b-allele counting occurs in parallel with the read counting phase, and the values are output in a *.baf.bedgraph.gz file. This file can be loaded into IGV along with other bigwig files generated by DRAGEN for visualization.