--minimum-allele-fraction does not work, vcf output is not filtered properly
REQUIRED for all errors and issues:
a) GATK version used: 4.2.6.1
b) Exact command used: gatk Mutect2 -R ref_seq.fasta -I snp50-x3.sorted.rg.MD.bam --minimum-allele-fraction 0.05 -O snp50-x3.sorted.rg.MD.vcf.gz > mutect2.log
c) Entire program log: (not sure how else to get the log)
Tool returned:
SUCCESS
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Hiral Desai Mutect2 does not do filtering; that is the job of FilterMutectCalls. Also, this argument is not an AF threshold for filtering variants, see the command line help docs for details. In any case, we do not recommend hard filtering in this manner.
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thank you, why is the argument available then? I also tried it for FilterMutectCalls and it does not work as intended. The expected results don't filter according to my set AF or AD.
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We do not recommend hard filtering by AF and AD. We recommend using the defaults for Mutect2 and FilterMutectCalls except in exceptional circumstances.
The argument works as intended but the intent is not filtering. It is a very technical detail of the mitochondrial GVCF mode that we needed for the gnomAD mitochondria project. -
I'm using it for viral variant calling and in my circumstance, I need to set more criteria based on ground truth data we've been studying. The command line options are available whether it's FilterMutectCalls or VariantFiltration but even if I add a filter flag such as AD < 3 and provide the expression PASS OR lowReads, the VCF output does not format accordingly.
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Viral variant calling could, possibly, be an exceptional circumstance. I'm not sure what argument you are referring to in FilterMutectCalls, but I believe that the VariantFiltration command would be something like:
gatk VariantFiltration \
-R reference.fasta \
-V input.vcf \
-O output.vcf \
--filter-name "lowReads" \
--filter-expression "AD < 3"
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