Evaluation of read alignment and variant calling methods.

<p><b>(A)</b> Comprehensive illustration of 441 evaluated read alignment results. Each method is referenced in standard, and in two additional, parameter settings. The plots show the number of aligned reads, where the range for each bar illustrates the observed variability when different lines were used. <b>(B)</b> Heat map depicts the true positive sites in the 50k array. A total of 504 combinations of read alignment and variant calling methods were evaluated to identify recommended or less optimal applications (genotype NC358). <b>(C)</b> Variant caller performance compared to the 50k array. The total number of identified SNPs, as well as the number of unique SNPs, is depicted for each of the eight evaluated methods (genotype NC358).