Question: Software for SNP analysis that can deal with ambiguities
0
gravatar for NoaG
2.6 years ago by
NoaG0
NoaG0 wrote:

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

snp sequence • 612 views
ADD COMMENTlink modified 2.6 years ago by EagleEye6.2k • written 2.6 years ago by NoaG0
1
gravatar for EagleEye
2.6 years ago by
EagleEye6.2k
Sweden
EagleEye6.2k wrote:

Freebayes, haplotype-based variant detector

https://github.com/ekg/freebayes

Regarding handling ambiguous sites

https://github.com/ekg/freebayes/issues/320

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by EagleEye6.2k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1543 users visited in the last hour