Structural Variation Detection Using Gatk

Question

[Pascal]

Hi. The GATK flow chart shows a "SV" box - along with SNPs and indels - in the possible outputs of the variant discovery phase. Nevertheless, reading the best practices and other documents there are only references to SNP and INDEL.

I'm curious to know the possibilities of SV discovery with GATK (e.g. CNV). Is it referrening to a third-party module?

Regards. Pascal

Answer 1

[User 59]

I think it might be referring to this

"Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovery and genotyping of structural variation using sequencing data. The methods used in Genome STRiP are designed to find shared variation using data from multiple individuals. Genome STRiP looks both across and within a set of sequenced genomes to detect variation."

This relies on the SVDiscovery and SVDiscoveryWalker parts of the GATK.