Problem to calculate fst by smartpca
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5.2 years ago
anahit ▴ 20

Hello guys! I want to ask you about smartpca program. I want to calculate fst values. Do you know what parameters exactly to include in the parfile. I was trying to use only genotypename,snpname, indivname and fstonly (YES) but i have no results in my output. Thank you in advance!

SNP • 2.3k views
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5.0 years ago
Simo ▴ 50

Hi anahit, this is what I usually do:

Open the file .fam and change the values in column 6.

You have to create groups by assigning a number to those individuals that belong to the same group, something like this:

ID1 A 0 0 1 3
ID1 B 0 0 1 3
ID2 C 0 0 1 4
ID2 D 0 0 1 4
...


It is important that you skip the number 1 and 2 (that are recognized as case and control), and number 9 that for some reason is not well accepted!

Once you have changed the file .fam, convert the bed/bim/fam to ped/map.

Prepare your par file with the option "fstonly: YES"

Run it with smartpca.

You'll end up with a file .phy showing the Fst matrix you want.

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Thank you so much, Simo!

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Hey man. Sorry to hijack this thread so late but queries regarding this were next to nothing. I have already changed my fam file according to your recommendations and converted it with convertf. However, I am not able to generate the file with the fst data. The following is my par file:

fstonly: YES
fstdetailsname: sogdia.greek.4.out
genotypename: sogdia.greek.4.geno
snpname: sogdia.greek.4.snp
indivname: sogdia.greek.4.ind
evecoutname: sogdia.greek.4.evec
evaloutname: sogdia.greek.4.eval
numoutevec:   20
numoutlieriter: 0
snpweightoutname: sogdia.greek.4.snpweight
killr2: YES
r2thresh: 0.75
outputgroup: YES


Also if you could point me towards how to exactly plot the data. Thank you so much.