Table 3 Heterozygous mismatch (a) between each call set and GWAS genotypes at 378 on-target markers, and (b) between additional heterozygous genotypes in more complex algorithms and the GWAS markers
From: Comparing variant calling algorithms for target-exon sequencing in a large sample
All samples at 378 GWAS markers | IBC | PBC | LDC | LDC + F | ||
|---|---|---|---|---|---|---|
(a) | Number of heterozygous genotypes (hets) | 276,761 | 293,730 | 298,220 | 298,531 | |
Heterozygous mismatch | 0.82% | 0.38% | 0.39% | 0.32% | ||
(b) | Number of additional hets and heterozygous mismatch | not in IBC | – | 15,727 (0.85%) | 17,937 (1.23%) | 18,308 (0.47%) |
not in PBC | – | – | 3,113 (2.41%) | 3,664 (0.71%) | ||
not in LDC | – | – | – | 1,145 (0.87%) | ||