Fig. 3
From: An analytical workflow for accurate variant discovery in highly divergent regions
Known SNPs in HLA-DRB1 and HLA-DQB1 from NA12878. The HLA-DRB1 (a) and HLA-DQB1 (b) structures are shown at the top, with filled boxes representing the exons (E1 to E6 in HLA-DRB1 and E1 to E5 in HLA-DQB1) and arrow indicating transcription direction. The exome-seq reads from NA12878 were mapped by BWA and GSNAP, respectively, and SNPs were called by GATK UnifiedGenotyper (GATK UG). Known SNPs matching dbSNP v138 are showed as ‘circles’ and clustered into three groups. Number in parentheses indicates the number of known SNPs in each group. The two coverage plots depict BWA and GSNAP mapping coverage at base-pair resolution