FilterMutectCalls failing filters
Can you please provide
a) GATK version used- 220.127.116.11
b) Exact GATK commands used-
java - jar ~/gatk-18.104.22.168/gatk-package-22.214.171.124-local.jar FilterMutectCalls \
-R fasta file \
-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!
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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