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GenomicsDBImport returns duplicate field error from SelectVariants output
I successfully ran Mutect2 using tumor-only mode with a PoN and germline resource. However, I didn't set the flag 'max-mnp-distance 0' meaning I get MNPs in my output. This results in GenomicsDBImport failing as it doesn't support MNPs.
OK, so I then ran SelectVariants with '--select-type-to-exclude MNP' to remove them and used this as input to GenomicsDBImport instead. However, it errors out with the message that duplicate field names exist (see below).
What should/can I do to correct this? I'd prefer not to have to run Mutect2 again if possible.