SNP Calling, Genotype Calling, and Sample Allele Frequency Estimation from New-Generation Sequencing Data
Figure 2
ROC curves for different SNP callers.
Data for 10 individuals were simulated assuming a sequencing depth of 2 and a raw sequencing error rate of 1% (A) and (B) a depth of 5 and a raw sequencing error rate of 5%. The SFS method is the main method described in the text. The GC method is based on genotype calling using the genotype with the highest posterior probability. The LR method is based on a likelihood ratio test of the hypothesis that the allele frequency is zero. The SFS based method and the LR method have similar performance except for very high error rates, where the SFS tends to be somewhat better. Both methods in general perform much better than the GC method. The difference would even larger in larger panels of individuals. Simulations under other conditions can be found in Figure S1.