From: SNPest: a probabilistic graphical model for estimating genotypes
Program | #SNPs | SNP rate | dbSNP | SNPest | Excl. | Indels | dbSNP | Homo:hetero |
---|---|---|---|---|---|---|---|---|
SNPest | 40,997 | 0.12% | 99.17% | 100.00% | 0.86% | 82 | 57.32% | 0.46 |
FreeBayes | 11,570 | 0.03% | 87.99% | 14.52% | 29.55% | 511 | 60.86% | 4.67 |
SAMtools | 43,679 | 0.13% | 99.37% | 96.92% | 0.40% | 3,880 | 57.45% | 0.49 |
GATK | 43,721 | 0.13% | 99.29% | 95.40% | 2.77% | 5,660 | 56.29% | 0.58 |
GeMS | 51,117 | 0.15% | 89.22% | 97.78% | 13.68% | N/A | N/A | 0.50 |