Can vcf file from mutect2 be used in RNAseq short variant discovery

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Robert Bremel

• July 13, 2020 02:44

Can you please provide
a) GATK version used
b) Exact GATK commands used
c) The entire error log if applicable.

Docker gatk:latest

The method suggested for RNAseq short variant discovery uses haplotypecaller on STAR-aligned and cleaned-up mRNAseq files.  One of the arguments for the haplotypecaller is --alleles: FeatureInput.     From what I can tell the "FeatureInput" is a vcf file.   

Does it make sense to use ann appropriately edited VCF from mutect2 as the FeatureInput to see whether the mRNA data has evidence (or not) of mutations detected?

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  Genevieve Brandt (she/her)

  • July 15, 2020 18:18

  Hi Robert Bremel, please see the documentation on HaplotypeCaller as well as the documentation for the best practices pipeline. It doesn't look like that option is part of best practices, and I also noticed it does not seem to call based on any evidence, but that option force-calls the given variants. "The set of alleles to force-call regardless of evidence."

  If other people in the community have used this option, please chime in!

  The GATK support team is focused on resolving questions about GATK errors and abnormal results, so for these type of questions, we are not able to guarantee an answer. Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

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  David Benjamin

  • July 24, 2020 13:58

  Robert Bremel Could you clarify what you are proposing?  My tentative understanding is that you want to run Mutect2 on your RNA seq data, then pass the Mutect2 output vcf to HaplotypeCaller via the force-calling (-alleles) option.  Do I have that right?

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