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Table 3 Increasing the prior heterozygous probability modestly improves concordance between exome and array genotypes

From: Reducing the exome search space for Mendelian diseases using genetic linkage analysis of exome 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

  1. 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.
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Genome Biology

ISSN: 1474-760X

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