Table 3

Increasing the prior heterozygous probability modestly improves concordance between exome and array genotypes

t

M-3 (N = 52,617)

M-4 (N = 52,892)

A-7 (N = 29,459)

T-1 (N = 32,763)


0.00001

0.9737

0.9734

0.9698

0.9741

0.001 (default)

0.9882

0.9874

0.9865

0.9885

0.01

0.9927

0.9926

0.9918

0.9925

0.05

0.9951

0.9950

0.9942

0.9945

0.1

0.9958

0.9958

0.9950

0.9952

0.2

0.9968

0.9965

0.9958

0.9961

0.3

0.9971

0.9968

0.9961

0.9964

0.4

0.9973

0.9971

0.9964

0.9968

0.5

0.9974

0.9973

0.9965

0.9969


Proportion of SNPs where WES and genotyping array genotypes are concordant for the four exomes, for varying values of t (prior probability of a heterozygous genotype). Conditional on coverage with ≥ 5 reads.

Smith et al. Genome Biology 2011 12:R85   doi:10.1186/gb-2011-12-9-r85

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