Figure 1.

Effects of read preprocessing steps on SNP calling. Number of mapped reads using different preprocessing steps for five samples (A). Venn diagrams comparing identified novel variants between the raw call set and the call set with the trim step. Number of unique novel SNPs, the Ti/Tv ratio and number of common novel SNPs were listed(B). Venn diagrams comparing identified novel variants between the call set with the filterY step and the call set with both filterY and trim steps. Number of unique novel SNPs, the Ti/Tv ratio and number of common novel SNPs were listed (C). Venn diagrams comparing identified known variants between the raw call set and the call set with the filterY step. Number of unique known SNPs, the Ti/Tv ratio and number of common known SNPs were listed (D). Venn diagrams comparing identified known variants between the call set with the trim step and the call set with both filterY and trim steps. Number of unique known SNPs, the Ti/Tv ratio and number of common known SNPs were listed (E).

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