Flowchart of the integrated genotyping procedure used to call SNP and non-SNP variants. Seven different variant calling methods were used to derive a consensus list of variant calls. The variant calls were grouped into haplotype bins (indicated by dashed vertical lines) such that there is a region on both sides of each region containing two or more regions of at least 110 bp with no non-SNP variants in any line. The variable regions and their 110-bp flanking regions were used to derive the sequences of alternative haplotypes against which reads are aligned. Finally, reads were aligned and genotypes called, followed by quality filtering that accounted for the experimental design.