Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

What is cohort?

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    Genevieve Brandt (she/her)

    Hi Linda Do,

    I would recommend a joint calling pipeline over a single sample pipeline for your case, as joint calling could offer some benefits when called together. You can also use the trio data to refine the calls with our genotype refinement methods.

    For our usage of cohort on this site, we mean group of samples. They do not all need to be affected.

    Best,

    Genevieve

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    Genevieve Brandt (she/her)

    Hi Linda Do,

    The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

    Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

    We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

    For context, check out our support policy.

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    Linda Do

    Thank you for your answer Genevieve Brandt.

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