FilterMutectCalls failing filters

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Elizabeth Schabot

• July 13, 2020 20:57

Can you please provide
a) GATK version used- 4.1.5.0

b) Exact GATK commands used-

java - jar ~/gatk-4.1.5.0/gatk-package-4.1.5.0-local.jar FilterMutectCalls \

-R fasta file \

--mitocondria-mode \

-V vcf file.gz \

-O vcf filtered file.gz

 

Hi I am new to using GATK and I have run the RNAseq best practices pipeline but have swapped out the HaplotypeCaller for Mutect2. I have used FilterMutectCalls on my VCF output from Mutect2 and I am trying to understand the results I received. Is there a concise file or document that explains what the failing filters from the filter column mean (I know there are brief descriptions in the header but I would like less opaque explanations)? If there is such a file or document will it also say which failing filter coordinates with certain arguments (I have found a few from multiple sources such as the base_qual is controlled by --min-median-base-quality)? Thank you!

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• 

  Genevieve Brandt (she/her)

  • July 23, 2020 20:58

  Hi Elizabeth Schabot, here is some of our documentation that might help you:

  • FilterMutectCalls documentation page
  • How to call somatic mutations Mutect2 tutorial (descriptions for what is going on)
  • Mutect2 paper
  • There is a video about the somatic mutations best practices which goes over the algorithms

  Hope this helps you get a better idea of the tool!

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