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

Using VSQR for somatic mutations?

0

8 comments

  • Avatar
    Bhanu Gandham

    Hi ,

    The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

    Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

    We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

    For context, check out our support policy.

     

    0
    Comment actions Permalink
  • Avatar
    David Benjamin

    I think VQSR would consider somatic variants with allele fraction near 1/2 to be germline, so it's not clear to me how this would work.  Perhaps you could explain further?

    0
    Comment actions Permalink
  • Avatar
    vctrymao

    I would agree, though I guess I was more generally wondering how Mutect addresses tumor-only calling, in terms of filtering out germline variants and artifacts.

    0
    Comment actions Permalink
  • Avatar
    David Benjamin

    I'm afraid there is no short answer to your question, but there is a long answer: https://github.com/broadinstitute/gatk/blob/master/docs/mutect/mutect.pdf.

    0
    Comment actions Permalink
  • Avatar
    vctrymao

    I have read that, but I don't see anything specific about Mutect's tumor-only mode. I was more curious as to how components like FilterMutectCalls works in that way. 

    0
    Comment actions Permalink
  • Avatar
    David Benjamin

    There's not much more to say about tumor-only mode than what's in the documentation.  It's Bayesian, so a region with zero reads in the normal (whether due to having no normal at all or due to lack of coverage in the normal) is just a specific case of the general model.

    0
    Comment actions Permalink
  • Avatar
    vctrymao

    Ok. Would you be able to explain this specific case? How does Mutect approach it using zero reads in the normal?

    0
    Comment actions Permalink
  • Avatar
    David Benjamin

    For example, any log likelihood ratio between an allele being present or absent in the normal is zero, since an absence of data has the same likelihood under any hypothesis.

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk