Overview
There are two factors to consider when deciding how to run GATK-SV.
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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:
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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.
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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).
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Which platform you would like to use for running GATK-SV? You may run GATK-SV on the following platforms.
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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.
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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.
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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.