Fig. 2
From: REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats
An overview of the pileup generation algorithm: A–C reads originating in the region containing target STRs are realigned using the sequence graph aligner within ExpansionHunter software; D, E putative pairs of haplotype sequences are generated from repeat genotypes; F a haplotype pair that has the highest consistency with read alignments is selected; G possible alignments of each read to each haplotype sequence are generated from the original sequence-graph alignments; and H pairs of read alignments that correspond to the most consistent fragment length are selected for each read pair and then one of these is randomly selected for visualization