Question: Any Simple Script To Calculate Fst Value Between Populations From Genomewide Snp Data (Available In Plink Format)
6
gravatar for User 0422
8.0 years ago by
User 0422150
User 0422150 wrote:

Hi All,

I am looking for a simple script which calculate the fst between different populations, taking input as PLINK files (either ped or bed).

Thanks

bed snp plink ped fst • 12k views
ADD COMMENTlink written 8.0 years ago by User 0422150

I'm surprised this hasn't been answered yet... want it too!

ADD REPLYlink written 7.6 years ago by pufferfish260
2
gravatar for Zach Stednick
7.6 years ago by
Zach Stednick650
Seattle, WA
Zach Stednick650 wrote:

Why not just use an existing program such as Genepop and write your own script to generate input files? Genepop provides plenty of example input files and once you have input your data it runs very fast.

ADD COMMENTlink written 7.6 years ago by Zach Stednick650
1
gravatar for Larry_Parnell
7.6 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

Because Fst calculations are so much less complicated than iHS, we take a very programmatic approach to Fst calculations for our SNP panels. We have written a program to do this in a high-throughput manner. My colleague wrote a script in R or Perl, but this is so simple that it could even be done in Excel.

ADD COMMENTlink written 7.6 years ago by Larry_Parnell16k

I'm looking to do some quick Fst calculations for a single SNP. I will use excel or a simple R script. I am looking for a good reference to an equation to calculate pair-wise Fst...

ADD REPLYlink written 4.6 years ago by Scott80
1
gravatar for Davy
7.2 years ago by
Davy210
Davy210 wrote:

The R package hierfstat can do this. As well as computing Fst values, it can group your populations and compute Fst values for the groups. Very flexible. For in the input file I think plink ped files may need some reworking as it's been sometime since I've used it but the vignette can help you with that. Also has some cool functions for generating sample SNP data to vary mutation and migration rates and things like that.

Documentation here: http://cran.r-project.org/web/packages/hierfstat/hierfstat.pdf

ADD COMMENTlink written 7.2 years ago by Davy210
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