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CNV calling and CNVR definition

JJ Jisung Jang
KK Kwondo Kim
YL Young Ho Lee
HK Heebal Kim
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CNVs of all samples were called with a bin size of 200 bp by CNVnator [62] and filtered with size (> 1 kb), p-value calculated using t-test statistics (< 0.001) and fraction of reads with zero mapping quality (MQ0 < 0.5). The CNVs in unplaced scaffolds were removed. A 50% reciprocal overlap between filtered CNVs was defined as copy number variation region (CNVR) using ‘CNV_overlap.py’ script on GitHub (https://github.com/bjtrost/TCAG-WGS-CNV-workflow) [63]. CNVRs found in more than two individuals were used for downstream analysis to minimize false-positive [64]. Copy number of each CNVR was calculated based on aligned read depth and normalized using CNVnator. The normalized copy number of neutral region from diploid autosome was assumed to be 2.0.

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