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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Robert Baldwin

• March 11, 2021 21:11

Hello,

I need to do some variant calling on 50 diploid fish genomes sequenced to ~10X. The reference is from the same species but a different population. In terms of genetic distance, the MASH distance between the samples and reference ranges from 0.006 - 0.007 whereas the distance between samples is around 0.002. For reference, the distance between any two humans is supposed to be around 0.001. So my samples diverge quite a bit from the reference compared to humans. But they aren't as divergent as what you might get from bacteria isolates. For the latter, I know that GATK does not work very well and the community uses other tools like SNIPPY which is based on bwa mem/freebayes pipeline. I was wondering whether GATK when perform well in my case or whether there's better alternatives. How divergent does the reference need to be from the samples before GATK starts under performing other callers? thanks - Robert

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  Bhanu Gandham

  • March 15, 2021 18:34

  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)

  • March 29, 2021 22:53

  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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