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

After SNPs and INDELs are extracted, can they be recombined later?

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    Genevieve Brandt (she/her)

    Hi Daniel Westcott, we do not support snpEff annotations anymore. 

    You may find helpful looking at our tools for Variant Manipulation (link here) as well as our tool for functional annotations (Funcotator).

    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 not able to guarantee a solution. Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

    If other community members have experience with recombining SNPs and INDELs, please post your thoughts here. 

    For context, check out our support policy.

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