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Combine phased calls from Mutect2

Hello, is there a way to have Mutect2 emit multi-nucleotide variants instead of multiple adjacent SNVs?

For example, consider this variant:

REF: AGGT
ALT: ATCT

Mutect will call the G/T SNP in position 2 as one line, and the G/C SNP at position 3 as another line. Then the fact that they are part of the same haplotype is indicated by the phasing information in the info column of the vcf.

I would prefer to have it call a multiple nucleotide variant: REF GG and ALT TC.

Can I get Mutect to do this? Or is there any post-processing tool you can recommend?

The reason for preferring MNVs instead of SNVs is that I am using ensembl-VEP to predict the protein consequences of the variants. In that case it's quite important to represent the actual haplotypes instead of stepping through variant sites one-by-one.

Thanks,
Patrick

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