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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

How do I ensure sequence context-dependent artifacts, such as for FFPE deamination, are filtered using the current version of GATK?



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    Jeremy Huang

    I'm having similar problems. I have a high-proportion of G>T and C>A calls in my vcf even after filtering and specifying ob-priors

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    Pamela Bretscher

    Hi ISmolicz,

    The -f1r2-tar-gz output of Mutect2 in more recent GATK versions replaces CollectSequencingArtifactMetrics. This file contains all of the information for orientation bias artifacts, including OxoG and FFPE deamination so there is no need to specify a specific artifact. The documentation is a little bit different because FilterMutectCalls uses a different model than FilterByOrientationBias but the filtering and output should be the same. Please let me know if you have any other questions or concerns.

    Kind regards,


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