Fig. 3
From: Best practices for variant calling in clinical sequencing
Visual review of copy number and structural variants. Each pane is an IGV screenshot of WGS for a proband (top), mother, (middle), and father (bottom). The top track for each sample is a histogram of sequence depth. Reads are viewed as pairs, with discordant pair alignments highlighted in color. a A homozygous ~ 4-kb del that appears heterozygous in the proband, homozygous in the mother, and absent from the father. Note the discordant read pairs suggesting a deletion (red) and visible change in read depth. b Homozygous deletion inherited from two heterozygous parents. c A heterozygous paternally inherited deletion with ambiguous end point by paired-end mapping resolved by visual inspection of read depth. d A maternally inherited tandem duplication. Note the increased read depth in the histogram and the discordant read pairs highlighted in green that span the original sequence and their tandem duplication