Something I don't think was clear from the documentation in the initial version of MixviR...
In cases of multiallelic sites (genomic positions with more than one variant in a sample), each variant should be split into a separate entry/line in the VCF file. So, the VCF entry(ies) for variants A & T at genomic position 1000 with Ref allele "C" in a sample should NOT look like...
chr1 1000 . C A,T
But instead should look like...
chr1 1000 . C A
chr1 1000 . C T
I'll get this clarified in the next version's documentation.
Mike