Fig. 1.

Box plot showing the change of INDEL calling sensitivity after local realignment. a–e Simulated datasets with 5x coverage. f–j Simulated datasets with 40x coverage. Local realignment was performed using 90 % of the preplaced INDELs. The change of INDEL calling sensitivity is calculated as the sensitivity after local realignment, subtracted by that after duplicate marking. For callers together with BWA, only datasets with 0.05–1 % divergence were used. GATK HC, GATK HaplotypeCaller; GATK UG, GATK UnifiedGenotyper