Question: How to perform fst test using SNPs frequency?
0
gravatar for Abdul Rafay Khan
10 days ago by
Karachi, PK
Abdul Rafay Khan1000 wrote:

How to perform fst test using SNPs frequency?

My data format:

SNPs           Pop1  Pop2     Pop3    Pop4    Pop4    Pop5    Pop6    Pop7
rs2740574   0.974   0.9448  0.7921  0.9625  0.9616  0.902   0.3556  0.9161
rs1751034   0.8906  0.7586  0.798   0.8457  0.8223  0.8081  0.7413  0.747
rs1414334   0.875   0.8453  0.7872  0.8831  0.857   0.8533  0.5555  0.9081
rs662799    0.849   0.8966  0.9005  0.9203  0.9311  0.8913  0.8791  0.8491
rs2359612   0.8021  0.5172  0.6431  0.6105  0.6305  0.628   0.7907  0.546
rs2228570   0.7969  0.5868  0.6478  0.6445  0.5927  0.5996  0.7847  0.5425
rs7196161   0.7917  0       0.5758  0.6141  0.6353  0.6194  0.5408  0.5418
snp fst • 65 views
ADD COMMENTlink written 10 days ago by Abdul Rafay Khan1000

This is a duplicate of a post you made a few days ago How to perform fst test using SNPs frequency?

ADD REPLYlink written 10 days ago by maxwhjohn198870

And is more or less identical to this from a few days before Minor allele frequency and fst test

ADD REPLYlink written 10 days ago by maxwhjohn198870
1
gravatar for maxwhjohn1988
10 days ago by
maxwhjohn198870 wrote:

There are too many pieces of software available to do this for someone to choose one for you. You should go onto google and search for solutions. Try some, and come back to ask for help if you need help getting one of the available pieces of software to work. Some starting points would be PopGenome (R package) and PoPoolation2 (for pooled sequencing data).

ADD COMMENTlink written 10 days ago by maxwhjohn198870

Thanks maxwhjohn1988 - I have closed the other threads.

Abdul, as per maxwhjohn1988, there are many programs that can do a FST test. Try the R package recommended by maxwhjohn1988.

ADD REPLYlink written 10 days ago by Kevin Blighe42k
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