Table 2 Heterozygous mismatch (a) between sequence calls and GWAS genotypes at 378 on-target GWAS markers, (b) between 80 sequence replicate pairs and (c) between pairs of algorithms
From: Comparing variant calling algorithms for target-exon sequencing in a large sample
Heterozygous mismatch rate | |||||
|---|---|---|---|---|---|
IBC | PBC | LDC | LDC + F | ||
(a) | All samples at 378 GWAS markers | 0.82% | 0.38% | 0.39% | 0.32% |
(b) | 80 sequence replicate pairs at all called variants | 1.01% | 0.34% | 0.36% | 0.20% |
(c) | Pairwise comparison of callers | ||||
vs PBC | 0.42% | -- | -- | -- | |
vs LDC | 0.93% | 0.35% | -- | -- | |
vs LDC + F | 1.01% | 0.41% | 0.30% | -- | |