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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

Question: Variant Calling when Genetic Distance between Reference and Samples is Greater than it is for Humans: Does GATK still perform well?



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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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    Genevieve Brandt (she/her)

    Robert Baldwin,

    We don't have any information to share about using GATK with fish genomes or any details about how genetic distance affects variant calls with HaplotypeCaller. Other factors besides genetic distance also play a role in variant calling and since we do not know about fish genomes, we cannot be sure what your results will be like.

    There are other users who have tried GATK with non-human use cases and you can check out these posts on the forum: Special GATK Use Cases topic. There are also some other posts that may not be in that category but in the Non-human topic.

    Please let us know what you find and if you have any recommendations for other people using GATK with fish genomes.

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