Best Practices Guide

A comprehensive guide for the single-sample calling mode is available in GATK Best Practices for Structural Variation Discovery on Single Samples. This material covers basic concepts of structural variant calling, specifics of SV VCF formatting, and advanced troubleshooting that also apply to the joint calling mode as well. This guide is intended to supplement documentation found here.

Users should also review the Getting Started section before attempting to perform SV calling.

The following sections also contain recommendations pertaining to data and call set QC:

• Preliminary sample QC in the EvidenceQc module.
• Assessment of completed call sets can be found on the MainVcfQc module page.