About

GATK-SV is a comprehensive, cloud-based ensemble pipeline to capture and annotate all classes of structural variants (SV) from whole genome sequencing (WGS). It can detect deletions, duplications, multi-allelic copy number variants, balanced inversions, insertions, translocations, and a diverse spectrum of complex SV. Briefly, GATK-SV maximizes the sensitivity of SV discovery by harmonizing output from five tools (Manta, Wham, cnMOPS, GATK-gCNV, MELT). In order to reduce false positives, raw SV are adjudicated and re-genotyped from read evidence considering all potential sequencing evidence including anomalous paired-end (PE) reads, split reads (SR) crossing a breakpoint, normalized read-depth (RD), and B-allele frequencies (BAF). It also fully resolves 11 classes of complex SV based on their breakpoint signature. GATK-SV has been designed to be deployed in the Google Cloud Platform via the cromwell execution engine, which allows massively parallel scaling. Further details about GATK--SV can be found in Collins et al. 2020, Nature.

A high-level description of GATK-SV is available here.

Citation

Please cite the following publication:

• Collins, Brand, et al. 2020. "A structural variation reference for medical and population genetics." Nature 581, 444-451.

Additional references:

• Werling et al. 2018. "An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder." Nature genetics 50.5, 727-736.