Joint Genotyping Methods

Table of Contents

• Breakpoint-resolved structural variant calls
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Breakpoint-resolved structural variant calls

All breakpoint-resolved calls released in Polaris have been jointly called on the using our SV breakpoint graph aligner and joint genotyping suite, paragraph.

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Breakpoint graph alignment

paragraph realigns reads to graph models of breakpoint-resolved structural variants or other complex genomic variants. Variants can be specified either in a JSON or — through a helper script — a VCF file. Specifications for the variant model JSON format are described here.

paragraph outputs a JSON , which provides the coverage for each node, edge, and path in the variant graph, and optionally provides all the alignments that were realigned to the graph with additional, graph-specific, alignment information.

SV joint genotyping

paragraph output JSONs are then used to derive a population-based model to call genotypes at a particular locus. Currently, a Poisson mixture model expectation maximization approach is used to make calls. Its output is a CSV file of genotypes for each sample at each breakpoint or variant in the variant model.