Table 2.
Call concordance with the 1000 Genomes Project (homozygous common allele)
|
Tool |
NA12763 _R |
NA12763 _R1 |
NA12763 _R2 |
|||
|---|---|---|---|---|---|---|
| Rate | Number | Rate | Number | Rate | Number | |
| GenCall (original) |
0.999478 |
114,975 |
0.999461 |
115,008 |
0.999486 |
114,876 |
| GenCall (optimized) |
0.999393 |
115,288 |
0.999384 |
115,288 |
0.999393 |
115,279 |
| GenoSNP (original) |
0.999630 |
97,236 |
0.998973 |
78,868 |
0.925482 |
74,210 |
| GenoSNP (optimized) |
0.999190 |
114,814 |
0.999138 |
114,910 |
0.999207 |
114,687 |
| optiCall |
0.998990 |
114,815 |
0.998972 |
114,805 |
0.999006 |
114,701 |
| zCall | 0.999281 | 115,438 | 0.999281 | 115,437 | 0.999290 | 115,438 |
Call concordance and number of compared markers for the three control replicates when compared to the 1000 Genomes Project. For each dataset (i.e. tool), only genotypes called as homozygous of the common allele (according to the allele frequency computed using the corresponding dataset) were kept for analysis. The following six tools were compared: GenCall (original and optimized cluster files), GenoSNP (original and optimized), optiCall (without excluding markers failing Hardy-Weinberg) and zCall.