Fig. 1.

Schematic procedure for indel realignment and haplotype clustering. (A) Flowchart with the overview of the process. (B) Voting mechanism to select the most likely start of a given indel. Blue bars represent aligned reads. The numbers on top represent the reads supporting each possible start position. (C) Realignment of reads supporting indel events according to the results of the voting procedure and clustering of candidate haplotypes to discover and genotype small indels. Reads that do not span across the indel (marked with X) are soft-clipped