Figure 2.

Effects of realignment, recalibration and marking duplication on SNP calling from high and low coverage data. Venn diagrams comparing identified novel variants between two call sets using different steps. Number of novel SNPs, the Ti/Tv ratio and number of common novel SNPs were listed in the comparisons between the initial call set and the call set with realignment step for high (A) and low (D) coverage data, between the initial call set and the call set with recalibration step for high (B) and low (E) coverage data, between the initial call set and the call set with marking duplication step for high (C) and low (F) coverage data.

Liu et al. BMC Genomics 2012 13(Suppl 8):S8   doi:10.1186/1471-2164-13-S8-S8