Joint Genotyping Methods

Table of Contents

• Small variants
• Breakpoint-resolved structural variant calls
  • paragraph
  • Depth-based CNV caller

Small variants

We have created a merged polaris dataset with gvcfgenotyper, a prototype for merging/genotyping samples from GVCF.

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.
• Depth-based CNV caller

Paragraph

Paragraph realigns reads to a graph model of structural variants breakpoints. A Poisson mixture model is used to make genotype calls for breakpoints and for the variant. Please check our Paragraph repository for details

Depth-based CNV caller

This method performs targeted calling of CNV genotypes using depth information. It consists of the following stages:

1. Read counts are derived from each targeted CNV region.
2. Proper event-length, sample-median and GC normalization are performed.
3. Normalized depth values in the population are modeled with a constrained one-dimensional mixture of gaussians to derive the final genotype calls.

Note that this method does not require the CNV breakpoints to be resolved to single nucleotide resolution.