Fig. 2

Change of SNP calling sensitivity after BQSR. a–c Datasets with 0.05–0.1, 0.5–1 and 5–10 % divergence, respectively, at 5x coverage. d–f Datasets with 0.05–0.1, 0.5–1 and 5–10 % divergence, respectively, at 40x coverage. The change of sensitivity is calculated as the sensitivity after BQSR using 90 % of the permuted SNPs, subtracted by that after local realignment using 90 % of the preplaced INDELs. For callers together with BWA, only datasets with 0.05–1 % divergence were used. GATK HC, GATK HaplotypeCaller; GATK UG, GATK UnifiedGenotyper