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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

Issues with FilterRNAMutationsNoPoN in RNA-Mutect Workflow for Tumour Mutational Burden Estimation


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    Gökalp Çelik

    Hi khushi ahuja

    This workflow is not part of our published workflows so our support will be very limited. Looks like the original workflow is tied to GATK version and Funcotator resource for that version. From one version to another we have changes in the resource files and Funcotator functionality that may be causing the differences in the output. Our recommendation would be to follow the workflow as the author suggested and try to obtain resource file for GATK Funcotator We may not provide additional support for the rest since the workflow is neither published nor endorsed by us. 


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