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

Funcotator Information and Tutorial Follow


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    Field -Ye Tian

    Dear GATK developers, 

    I have processed a pair of Tumor/normal tissues that are WES'ed. I have followed the whole process of analysis and acquired the annotated .maf result. After going through it, I didn't see a column that's dedicated to the credibility of each variant. 

    I recall that when I used the VarScan2, it assigned a P value for each variant. It is calculated somehow by the number of reads supporting either the reference or the alternate from both the tumor and normal samples. I wonder if Mutect2 did the same and if I missed it. 


    Thank you very much. 


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    David Lord

    I believe there is a typo in the README file in the v.1.7 somatic data source package. The "use case" clearly states "somatic", however, the introduction starts with: "This is a collection of data sources to be used in conjunction with Funcotator to annotate Germline data samples."

    Thank you for providing the pre-packaged data sources and the downloader tool, saved me a whole bunch of time! :) 

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