Software for SNP analysis that can deal with ambiguities
Hello,
I'm studying 3 different genes in Goats. I've sequenced them all (Not NGS data), and now I'm looking for software that can deal with the Heterozygote (the ambiguities), as I want to analyse the Haplotypes, Relatedness and Fst. I tried the DNAsp, and Arleqin, but can't find the option for them recognise the ambiguities.
Do you know if there is an upgrade or other software that can take in count the ambiguities?
Thanks a lot
Noa
1 answer
Freebayes, haplotype-based variant detector
https://github.com/ekg/freebayes
Regarding handling ambiguous sites
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