Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

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

2 comments

  • Avatar
    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. 

     

    0
    Comment actions Permalink
  • Avatar
    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! :) 

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk