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

RNAseq short variant discovery (SNPs + 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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    Peiwen Li

    Hi Jay Singh,

    I have the some question. Did you figure out which variant caller to use for somatic RNAseq data, HaplotypeCaller or Mutect2?



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    Pamela Bretscher

    Hi Jay Singh and Peiwen Li,

    The current pipeline for RNA-seq variant discovery is focused on germline variants, which is why HaplotypeCaller is recommended. However, Mutect2 may be the correct choice when analyzing somatic variants. Here is a link to a discussion post about Mutect2 for RNA-seq with some suggestions and considerations from one of the GATK developers: There isn't currently a best practices for somatic RNA-seq but I hope you find this helpful.

    Kind regards,


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