Workflow from Scientific Research

Schematic of the haplotype deconvolution approach to infer the pair of structural haplotypes present in a short-read-sequenced individual. A set of assembled haplotypes are mapped to a variation graph, and coverage vectors are quantified over all nodes of the graph (1). Synthetic genotype vectors are constructed from summing all pairs of haplotype vectors (2). A short-read genome is mapped to the variation graph, and the read depth is quantified over all nodes in the graph (3). The short-read coverage vector is compared with all synthetic genotype vectors (4) and scored to identify the most likely haplotype pair present in the short-read-sequenced individual (5).

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