Fig. 4

Change of variant calling sensitivity after local realignment and BQSR in NA12878. a–b Change of INDEL calling sensitivity after local realignment in the HLA (a) and non-HLA regions (b). c–d Change of SNP calling sensitivity after BQSR in the HLA (c) and non-HLA regions (d). NA12878 exome-seq data NA12878_04 (approximate 100x coverage, Additional file 2: Table S1) was downloaded from https://basespace.illumina.com/and down-sampled into 40, 20 and 10x coverage. Change of sensitivity is calculated as the sensitivity after BQSR, subtracted by that after local realignment, or as the sensitivity after local realignment, subtracted by that after duplicate marking