Before performing CNV detection, we converted mapping data into the BAM format and removed gaps in the reference genome. CNVs were detected using an event-wise testing method based on read depth46. This method estimates the coverage of read depth in 100 bp non-overlapping windows and then performs significance testing. In this study, CNVs were defined as having at least 10 consecutive windows (100 bp each) with a minimum size of 1 kb. Merged events were filtered stringently at a significance level of 10−6.
