How to perform fst test using SNPs frequency?
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5.0 years ago

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 • 1.1k views
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This is a duplicate of a post you made a few days ago How to perform fst test using SNPs frequency?

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

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5.0 years ago
maxwhjohn1988 ▴ 130

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).

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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.

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