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broadinstitute / gatk

Official code repository for GATK versions 4 and up
https://software.broadinstitute.org/gatk
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[Mutect2] How to emit only one alt allele,not multi-allele? #6603

Closed xiucz closed 4 years ago

xiucz commented 4 years ago

Hi , The parameter --max-alternate-alleles seems no longer in the new version gatk4.1.7.0...How can I get only one alt allele in the vcf, or how to filter it?

Thank you, Xiucz

davidbenjamin commented 4 years ago

FilterMutectCalls has always and continues to filter multiallelics by default, except in mitochondria mode. You may adjust this with the max-alt-allele-count argument. -max-alternate-alleles is a HaplotypeCaller argument that appeared in Mutect2 due to excess inheritance in the class hierarchy. I don't believe it ever had any effect in Mutect2.

xiucz commented 4 years ago

I see the max-alt-allele-count argument in FilterMutectCalls now. But maybe it is used to filter the multiallele sites.

Sometimes, when I want to force call some cosmic hotspot sites in Mutect2 GGA mode, this parameter may be helpful.

Thank you.

davidbenjamin commented 4 years ago

We're moving in a direction where FilterMutectCalls can decide which alleles in a multiallelic site to keep, but because multiple alleles are such a strong signal for filtering I don't think we would want Mutect2 to silently drop alleles, except those that are obvious sequencing errors as in the current case. This HaplotypeCaller argument isn't anything principled; rather it keeps down computational costs.