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CombineVariants Key . found in VariantContext field INFO but this key isn't defined in the VCFHeader

I have encountered the following error when trying to merge two VCFs from different callers:

Key . found in VariantContext field INFO at chrM:711 but this key isn't defined in the VCFHeader. We require all VCFs to have complete VCF headers by default.

From looking at the VCF inputs, I can see that one of my VCFs has . as its INFO field (it's an output from Mutect 1). However, according to the VCF spec, this is a valid placeholder value.

I have attached the output log from this command, as well as the two VCFs.

Is this the correct behaviour? How can this error be avoided?

Answers

  • SheilaSheila Broad InstituteMember, Broadie admin

    @Migwell
    Hi,

    Have a look at this thread.

    -Sheila

  • MigwellMigwell Member

    That thread seems to recommend adding the key to the header, but in this case the key shouldn't need to be there since it's part of the VCF spec.

    I can look into GATK4 but it's very difficult for us to upgrade versions at the moment.

  • SheilaSheila Broad InstituteMember, Broadie admin

    @Migwell
    Hi,

    I think the issue is that it is not defined in the header, not that the . is actually part of the VCF. So, if you add the description to the header, it should work. Unfortunately, since we are in Mutect2 in GATK4, any bugs in MuTect1 will not be fixed. I hope you will be able to try GATK4 soon, as the Mutect2 in it is better than in GATK3 as well.

    -Sheila

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