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