Table 3 |
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|
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. |
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|
Smith et al. Genome Biology 2011 12:R85 doi:10.1186/gb-2011-12-9-r85 |
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