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

Somatic Mutation and PON creation



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    Genevieve Brandt (she/her)

    Hi avrajit,

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

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



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    Pamela Bretscher

    Hi avrajit,

    As long as the normal samples are similar preparation and sequencing methods to the tumor samples, it is encouraged to include normal samples from healthy individuals as a larger panel of normals will generally improve the accuracy of variant calling. You can reference our documentation on creating a panel of normals here.

    Kind regards,


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    Hi Pamela,

    Thanks for your response. I also thought the same. Just looking for a confirmation. Thanks a lot.

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