Include ambiguous bases but not Ns

[GonzaloYebra]

Hi! I know there's been a few similar issues raised here but they didn't match quite exactly what I'm looking for...

My question is, would there be any way to run snp-dists including ambiguous bases in the calculation while disregarding Ns? Basically a hybrid between the default and the -a options.

In my case, I wouldn't mind what specific ambiguous base is found, I'd like to count them all as different to ATCG.

Any ideas?

Thanks a lot!

Gonzalo

[tseemann]

@GonzaloYebra
Normally a match is +1 and a mismatch is 0.
How do you want the ambiguous IUPAC codes measured?

A vs R = 0
C vs R = 0
A vs N = 0
R vs R = 1 <---- ?
N vs R = 0

Is that correct?