Question: How to calculate Hudson's Fst at Population and SNP level?
1
gravatar for bibb77
4.6 years ago by
bibb7780
Chile
bibb7780 wrote:

Dear BioStars community:

I would like to know if there is a software or script that calculates Hudson's Fst estimator (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1205159/) at both Population and SNP level, the first to asses genetic distance between population and the second to detect highly divergent SNPs. I have used the EIGENSOFT software but this only produces Fst values at population level (pairwise matrix), but not for single SNPs. I also have used the well known method from Weir and Cockerham implemented in PLINK, but Bhatia et al, 2013 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3759727/#B16) recommends to use Hudson's estimator because it behaves better with uneven population sizes.

Thanks in advance.

ADD COMMENTlink modified 12 months ago by Mr Locuace90 • written 4.6 years ago by bibb7780
1
gravatar for alexisdereeper
3.5 years ago by
alexisdereeper30 wrote:

Using a VCF file as input, SNiPlay implements VCFtools that calculates Fst (Weir and Cockerham’s) for each marker... http://sniplay.southgreen.fr/cgi-bin/analysis_v3.cgi

ADD COMMENTlink written 3.5 years ago by alexisdereeper30
0
gravatar for gideond
4.4 years ago by
gideond0
United States
gideond0 wrote:

Hi there,

Any updates on this? Did you find something useful? Or implement the estimator yourself? I found this: https://bio.cst.temple.edu/~hey/program_files/Sites/SITES_Documentation.htm but it doesn't look well maintained and I am pressed to find actual usage examples in the documentation.

I'm thinking about implementing a simple version myself.

Hope to hear your thoughts.

ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by gideond0
0
gravatar for gideond
4.4 years ago by
gideond0
United States
gideond0 wrote:

The second paper you mentioned actually links to a software package called EIGENSOFT. It is available here: http://www.hsph.harvard.edu/alkes-price/software/. I have to admit that this has not made things any easier for me as I do not understand what a block-jackknife estimator is and there is no mention of Hudson estimators anywhere in the documentation (or source code). I'll continue keeping you posted.

ADD COMMENTlink written 4.4 years ago by gideond0

I was also frustrated by the lack of detail in the documentation--I see no mention of the type of Fst estimator.

ADD REPLYlink written 14 months ago by mellissa.demille10
0
gravatar for sinorenjianyi
3.6 years ago by
sinorenjianyi40 wrote:

Try this http://spsmart.cesga.es/

ADD COMMENTlink written 3.6 years ago by sinorenjianyi40
0
gravatar for Mr Locuace
12 months ago by
Mr Locuace90
Chile
Mr Locuace90 wrote:

https://www.rdocumentation.org/packages/KRIS/versions/1.1.1/topics/fst.each.snp.hudson

ADD COMMENTlink written 12 months ago by Mr Locuace90
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