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

`FilterMutectCalls` for normal only calls

0

3 comments

  • Avatar
    Genevieve Brandt (she/her)

    Hi AMN,

    The panel of normals is meant to be a source listing technical artifacts from the normals (source). Thus, the VCF should not be filtered after running Mutect2. We have done rigorous testing on the method to create the panel of normals and this is the method that gets the best reliable results with Mutect2.

    Best,

    Genevieve

    1
    Comment actions Permalink
  • Avatar
    AMN

    That's quite helpful, thanks! I am still concerned about cases like the one I mentioned, but it is good to know that overall this gave you the best results.

    0
    Comment actions Permalink
  • Avatar
    Genevieve Brandt (she/her)

    Glad it was helpful! I will keep your question regarding the clustered events in our backlog to ask the developers. There are a few events in the next few weeks so I probably won't get an answer soon.

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk