Structural Variant Calling

The DRAGEN Structural Variant (SV) Caller integrates and extends Manta structural variant calling to provide SV and indel calls 50 bases or larger. SVs and indels are called from mapped paired-end sequencing reads. The SV caller is optimized for analysis of diploid germline variation in small sets of individuals and somatic variation in tumor-normal sample pairs.

The SV caller performs the following actions:

•

Discovers, assembles, and scores large-scale SVs, medium-sized indels, and large insertions within a single efficient workflow.

•

Combines paired and split-read evidence during SV discovery and scoring to improve accuracy, but does not require split-reads or successful breakpoint assemblies to report a variant in cases where there is strong evidence otherwise.

•

Scores known SV deletions and insertions from an input VCF file against one or more input samples, either as a standalone procedure or together with standard SV discovery.

•

Provides scoring models for germline variants in small sets of diploid samples and somatic variants in matched tumor-normal sample pairs.

There is experimental support for analysis of unmatched tumor samples as well. All SV and indel inferences are output in VCF 4.1 format.