RNAseq short variant discovery (SNPs + Indels)

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Jay Singh

• May 12, 2020 18:30

In the RNAseq short variant discovery (SNPs + Indels) pipeline HaplotypeCaller is mentioned for variant calling.

I am using somatic data (RNA seq Data) of cancer patient for variant calling.

Should I use Haplotype Caller or Mutect2 ?

Thanks and Regards

 

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  Bhanu Gandham

  • May 15, 2020 17:04

  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

  • April 21, 2021 23:54

  Hi Jay Singh,

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

  Thanks,

  Peiwen 

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  Pamela Bretscher

  • September 03, 2021 13:32

  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: https://gatk.broadinstitute.org/hc/en-us/community/posts/360056152451-Mutect2-for-RNA-seq- There isn't currently a best practices for somatic RNA-seq but I hope you find this helpful.

  Kind regards,

  Pamela

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