Fig. 1.

Cartoon shows two samples (red and blue) and a diverged reference genome (black) in a de Bruijn graph; symbols indicate which workflows call sites. Brackets indicate flanking regions cannot be placed on reference, so the call is filtered from VCF. At SNP B, the independent workflow would call the red and blue versions of H and would implicitly find B. C is only called if the reference is excluded from discovery, as it confounds the red allele. D is called by workflows that include the reference in discovery