Reducing INDEL calling errors in whole genome and exome sequencing data

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

	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%

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.

ISSN: 1756-994X