MuTect2 and Alternate Allele Calls

Hi there,

We have a few calls in our dataset that are slightly confusing. We are getting a triallelic flag, which is expected, but only getting one alternate allele outputted to the VCF. The alternate allele that is being called is at <1% VAF, whereas the other alternate is in the 35-40% range, and is a common somatic variant. Any ideas on how to force the calling of these more frequent alternate alleles?