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Overview

There are two factors to consider when deciding how to run GATK-SV.

  1. Variant calling modes: single-sample and cohort-based calling. GATK-SV offers two distinct pipeline configurations for detecting structural variations (SVs), each tailored for different research needs:

    • Single-sample analysis: This configuration is ideal for examining SVs in individual samples, focusing exclusively on data from that single sample. Running this mode is less complex, involving just one workflow per sample.

    • Joint calling: This configuration is designed for more extensive studies, such as those involving population genetics or disease association studies. It analyzes SVs across a cohort by collectively assessing data from all samples. However, this comes with increased complexity compared to the single-sample mode, requiring the execution of multiple workflows and involves data preparation steps (e.g., batching files from the cohort).

  2. Which platform you would like to use for running GATK-SV? You may run GATK-SV on the following platforms.

    • Terra.bio: A user-friendly cloud-native platform for scalable data analysis. The primary focus of this documentation is on supporting the execution of GATK-SV within the Terra platform.

    • Cromwell: You may run GATK-SV on a self-hosted and managed cromwell instance, which is ideal for power-users and developers. We provide guidelines for this option in the advanced guides section.

Your decision regarding the execution modes and platform should be guided by the objectives of your study, the size of your cohort, data access needs, and the trade-off between a straightforward interface (Terra) and more detailed customization options (self-managed Cromwell server). Please refer to the following documentation on running GATK-SV within the Terra platform.