Table 1 Genotype concordance between WES genotypes and exome array genotypes in 10 samples
Filters | Number of concordant genotypes | Number of discordant genotypes† | Concordance | % of concordant genotypes removed | % of discordant genotypes removed | |
|---|---|---|---|---|---|---|
Genotype | Variant | |||||
None | None | 73,537 (621,855) | 551 (661) | 99.26% (99.89%) | NA | NA |
None | VQSR | 73,069 (608,065) | 493 (108) | 99.33% (99.98%) | 0.64% (2.22%) | 10.53% (83.66%) |
DP | None | 72,104 (611,606) | 236 (627) | 99.67% (99.90%) | 1.95% (1.65%) | 57.17% (5.14%) |
GQ | None | 72,689 (610,682) | 225 (460) | 99.69% (99.92%) | 1.15% (1.80%) | 59.17% (30.41%) |
DP & GQ | None | 71,986 (610,108) | 220 (446) | 99.70% (99.93%) | 2.11% (1.89%) | 60.07% (32.53%) |
DP & GQ | VQSR | 71,552 (597,070) | 168 (36) | 99.77% (99.99%) | 2.70% (3.99%) | 69.51% (94.55%) |