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

Shared variants

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    Genevieve Brandt (she/her)

    Hi Priya,

    You can use custom filtering methods with our tools VariantFiltration or SelectVariants. You might also be able to find this out with other VCF analysis tools out there.

    Other users who have done something similar may be able to share the specific commands they used. I did find one post on biostars that might be helpful in figuring this out:

    https://www.biostars.org/p/229022/

    Best,

    Genevieve

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    Genevieve Brandt (she/her)

    Hi Priya,

    I am going to move your post into our Community Discussions -> General Discussion topic, as the Germline topic is for reporting bugs and issues with GATK.

    You can read more about our forum guidelines and the topics here: Forum Guidelines.

    Best,

    Genevieve

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