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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

GATK CNV somatic panels of normal design



  • Official comment
    Genevieve Brandt (she/her)

    Hi Mallika Gandham,

    Thanks for writing into the GATK forum with these questions! Here are the responses for each question:

    1. Yes, even though it's a small panel of genes, 40 samples is still enough. Reducing the number of genes will not reduce the quality because each gene is independent.
    2. We would recommend being careful with this approach, specifically with FFPE samples. FFPE can have many unmappable reads which could start to effect what your CNV data looks like. It could potentially be okay if these FFPE samples are high quality. But it might be extra challenging if you are also trying to combine sample types.
    3. This is not recommended, only if you are truly positive they have no CNVs. If they do have CNVs, it will not be good for the results.
    4. These two differences should not be a problem 
      1) This would just result in a multiplier of the read count, so it wouldn't be an issue
      2) We're not really familiar with the different flowcell types but even if it changes something in the normals, it could be helpful for the model
    5. For somatic CNV analysis, we don't store any publicly available PONs. The PONs for depth denoising of somatic samples should be generated using normal samples from similar sequencing technology and sample preparation. A generic PON does not do a good job, especially since the target sets for WES should be matching. 
    6. No, we don't do this because the germline CNVs will be removed from the samples anyway.
    7. GATK somatic CNV pipeline can perform well on a wide range of purities. The more pure the better, but we don't have a specific cutoff for usage of the pipeline.

    Please let us know if you have any other questions.



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    Genevieve Brandt (she/her)

    Thank you for your post, Mallika Gandham! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. 

    Please see our Support Policy for more details about how we prioritize responding to questions. 

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    Mallika Gandham

    Hi Genevieve-Brandt-she-her Thank you for the response. 

    Just need a bit of clarification on

    Question 6) 

    Is there a way to exclude samples from a Panel of Normals using CreatePanelofNormals module based on the profile of test samples being normalized? profile here I mean sample source,  etc. 


    And to add to that 
    Does GATK's CreatePanelofNormals exclude normals if they don't meet certain criteria?  

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