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Table 3 Validation rates of WGS-WES intersection, WGS-specific, and WES-specific INDELs

From: Reducing INDEL calling errors in whole genome and exome sequencing data

  INDELs Valid PPV INDELs (>5 bp) Valid (>5 bp) PPV (>5 bp)
WGS-WES intersection 160 152 95.0% 18 18 100%
WGS-specific 145 122 84.1% 33 25 75.8%
WES-specific 161 91 56.5% 1 1 100%
  1. We also calculated the validation rates of large INDELs (>5 bp) in each category. The validation rate, positive predictive value (PPV), is computed by the following: PPV = #TP/(#TP + #FP), where #TP is the number of true-positive calls and #FP is the number of false-positive calls.