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

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    Kate Herman

    This question was answered during our live webinar. The answer is copied below for posterity.


    A: Each of the model based filters uses the data you provide to M2 and FilterMutectCalls. As an example, the read orientation filters use statistics collected from LearnReadOrientationModel. These statistics are plugged into a model that is then used to filter variants.

    We don’t use a training set that explicitly labels true and false variants.

    - Mark Fleharty

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