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

Using LearnReadOrientationModel produces new mutations?

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    Bhanu Gandham

    Hi ,

    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.

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    David Benjamin

    vctrymao This is possible.  FilterMutectCalls sets a threshold on the posterior probability that variants are real by optimizing the estimated F score, which is the harmonic mean of sensitivity and precision.  When variants are correctly filtered out as orientation bias artifacts, FilterMutectCalls may nudge the threshold a bit lower in order to get a bit more sensitivity.  I would hope that all of the new PASS variants are borderline calls.

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