Dear Sean,
Ambiguity codes in migrate date back to sequence data sets where the IUPAC ambiguity code is used to describe uncertainty.
The ambiguity code in migrate is not used to mark a heterozygote it is used to inform the tree likelihood that we are not sure what
particular nucleotide it is. Therefore the use of ambiguity codes for snps is not useful because it simply says that we do not know which of the two
alleles should be used, your VCF with genotype data actually should emit both alleles and not just one, that could be used to generate two lines in the migrate infile so that in the VCF two individuals with AA, AC would translate in migrate to
one:1 A
one:2 A
two:1 A
two:2 C
The frequency spectra output is inconsequential for the analysis if it prints
W
A
T
that does only affect the frequency tables, but not the run and the Bayes posterior tables.
In the run the likelihood will be calculated from the conditiional tip likelihoods that are set up
using W, A, and T, so your heterzygote is expressed as uncertainty.
If you use large numbers of snp loci
set the parmfile option (you need to edit the parmfile, te menu does not include this) pdf-terse to
pdf-terse=YES
this may help to remedy issues with too large PDF files (that then crash).
Peter
P.S. Eventually migrate will be able to handle VCF data directly, but it is still a long way to go.