Genome Analysis Toolkit

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

Genotyping precalled sites/variants



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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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    Hi Reto,

    You can actually provide a list to GenotypeGVCFs to opporate on, it's the -L function. You can specify in that list single sites. I haven't tried it, but otherwise you could take a region of 100 bp before and after the variant you definitely want to call.

    for example you can format it as such, and save it as a list:

    for a site:

    for a region:

    I haven't tried this myself, but I think it should work. Also if the site isn't a variant in your new vcf it will not appear (unless you say --include-non-variant-sites this will ensure that you have all callable site)

    I hope this can help you :)


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    Bhanu Gandham

    ABours you are right -L can be used to restrict tool to certain sites. You can even provide vcf as input to -L.


    Thank you so much ABours for pitching in and helping out the GATK community! We appreciate your help with building the GATK Knowledge-base!

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