FreeBayes does not deal with ambiguous nucleotides -- what are good alternatives?

Question

[Lina F]

Hi all,

I am interested in calling SNPs for a set of yeast NGS data (paired-end reads). I followed a tutorial that recommends using FreeBays, but I am running into problems because my reference contains non-ATGC nucleotides (Ys, Ws, Ms, etc).

What is a good alternative to FreeBayes that's open source?

I checked out VG but the instructions seem very cryptic and there is little documentation that I can see.

Thanks for any advice!

[WouterDeCoster]

I can imagine that's not straightforward to do variant calling with ambiguous nucleotides in the reference genome. You absolutely have to use that reference? I'm entirely ignorant to yeast genetics, but I can't imagine all reference genomes contain ambiguous nucleotides...