Fig. 1. Overview of Integrating BAF and CNV Analysis Using VizCNV.

a) Demonstrates the methodology for trio-based joint calling and the classification of B-alleles. b) Outlines the approach for analyzing log₂ ratios and categorizing CNVs. c) Illustrates the combined analysis and visualization process using phased BAF and log₂ ratio data for de novo duplication and deletion, homozygous duplication and deletion (left to right). For a de novo duplication occurring on the maternal allele, we would expect a log₂ ratio of log₂(3/2) in the proband’s read depth plot, accompanied by phased BAF values of approximately 0.66 for SNVs phased to the maternal allele and 0.33 for those phased to the paternal allele. For a de novo deletion on the maternal allele, we would anticipate a log₂ ratio of log₂(1/2) in the proband’s read depth plot, with the paternal phased BAF near 1, resembling a ROH similar in size to the deletion, or an allelic imbalance pattern if the deletion is mosaic. In the case of a homozygous duplication, we would expect a log₂ ratio of log₂(3/2) in both parents and log₂(4/2) in the proband, with the duplication overlapping a larger ROH region. For a homozygous deletion, the expected log₂ ratio would be log₂(1/2) in both parents, with no signal in the proband, and the deletion would overlap a larger ROH region.