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

If it is OK when I run GenomicsDBImport on each chromosome

Answered
0

4 comments

  • Avatar
    Genevieve Brandt (she/her)

    Hi Lave,Guo,

    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
    Lave,Guo

    What if I use 'CombineGVCFs' to joint all my samples(not many)firstly and then run CreateSomaticPanelOfNormals with the merged VCF?

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

    Lave,Guo please see the best practices resources on this site for more information. 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.

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

    Hi Lave,Guo,

    I wanted to come back to your question because I'm not sure that we resolved your issue. Our recommended method for building a Panel of Normals can be found in this document: https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2

    If your question still remains unanswered, please could you clarify for me? I'm not sure I understand what you are asking.

    Best,

    Genevieve

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk