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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?