Figure 3:

CNVpytor workflow and steps used in data processing. Left: Reading RD data from alignment file, creating histograms, segmentation, calling CNVs. Right: Reading SNP and indel data from VCF file, filtering variants using strict mask, calculating histograms and likelihood function. Middle: Alternatively, if alignment file is not available, RD signals can be calculated from variant data (green arrows). Visualization using both RD and/or BAF data can be done from an interactive command line interface or automatically by running script file.