DRAGEN SV Caller Overview

The DRAGEN SV Caller divides the SV and indel discovery process into the following two primary steps:

1.

Scans the genome to build various genome-wide data structures, including a breakend association graph of all SV associated regions. The graph contains edges connecting all regions of the genome that have a possible breakend association. Edges can connect two different regions of the genome to represent evidence of a long-range association, or an edge may connect a region to itself to capture a local indel/small SV association. These associations are more general than a specific SV hypothesis and many breakend candidates may be found on one edge. Typically only one or two candidates are found per edge.

2.

Analyzes breakend association graph to discover candidate SVs, then scores discovered candidate SVs and any known SVs from the input. Analysis and scoring is performed as follows.

a.

Inference of SV candidates associated with the given graph edge.

b.

Attempted assembly of the SVs breakends.

c.

Scoring/genotyping and filtration of the SV under various biological models (currently diploid, germline, and somatic).

d.

Output scored SVs to VCF.