Fig 1. Workflow for selecting error-prone variants.

This workflow shows the steps used to select the error-prone variants from 27 VCF (Variant Call Format) files of WES data. The number of loci excluded after each filtering step is indicated. The loci remaining after the filtering steps were classified into four distinct error types, which were considered to be false positives. Note that a locus could be classified into multiple categories if it satisfied multiple error-prone conditions. A call was a highly likely false positive (HLFP) when both experts agreed it was a false positive, a likely false positive (LFP) when the two experts disagreed, and a likely true positive (LTP) when both experts agreed it was a true positive call. Cohen’s kappa coefficient (κ) for the correlation between the two experts was 0.6513.