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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

How do I choose the "optimal" VQSR sensitivity threshold for indels?

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    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.

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    Genevieve Brandt (she/her)

    Hi Degang Wu,

    Unfortunately, we don't have any information regarding a good sensitivity threshold. We are generally conservative with this, however.

    Other GATK users can weigh in on what has worked for them in the past.

    Best,

    Genevieve

     

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    Degang Wu

    If guideline on sensitivity threshold for indel VQSR model is not available, how about a threshold on VQS LOD?

    Any suggestions are welcome.

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    Genevieve Brandt (she/her)

    Hi Degang Wu, have you seen our document regarding filtering SNPs and Indels using VQSR or hard filtering? There is a lot of good information about how to make decisions with your own data. 

    Please let me know any specific points of confusion in that article so I can put in a documentation request with our team.

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    Degang Wu

    Hi Genevieve Brandt, I read the document in that link before, and I have just gone through it again in case I missed updates to the document. The document does not address my question. The document elaborates on how to build a VQSR model (or alternatively how to hard filter variants). My question is, supposed I have built a reasonable VQSR model for variants (addressed by the document you mentioned), what criteria should I use to choose a reasonable sensitivity threshold? For SNPs, we can decide based on the change of TiTv. For indels, there is no TiTv.

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    Genevieve Brandt (she/her)

    Thank you for the feedback, Degang Wu, I will put in a request to have that information added if possible.

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