FST details (by SNP FST) not printed

[TaniaPGue]

Hi!
I've been trying to get FST estimates per variant. I'm using the flag "fstdetailsname" as shown below, which I thought would do that, but I still only get the overall FST estimate. I tried other configurations but so far I only get that one line of output.
I would be very grateful for any help on this :) thank you!

My par file looks as follows:
genotypename: phased_panel.snpOnly.targetPopFiltered.ped
snpname: phased_panel.snpOnly.targetPopFiltered.map
indivname: AMR_EAS_EUR_poplist.ind
poplistname: AMR_EAS.EIGEN.list
fstonly: YES
fstdetailsname: FSTdetails.out
phylipoutname: FSTmatrix.phy

Output:
Fst statistics between populations: fst fstjack std error Z snpnumber
F_st AMR EAS 0.004445 0.004445 0.000254 17.467 3595170

[bumblenick]

Please retry with fstonly: NO

…

Sent from my iPhone

On Apr 3, 2024, at 6:20 PM, Tania Guerrero ***@***.***> wrote:  Hi! I've been trying to get FST estimates per variant. I'm using the flag "fstdetailsname" as shown below, which I thought would do that, but I still only get the overall FST estimate. I tried other configurations but so far I only get that one line of output. I would be very grateful for any help on this :) thank you! My par file looks as follows: genotypename: phased_panel.snpOnly.targetPopFiltered.ped snpname: phased_panel.snpOnly.targetPopFiltered.map indivname: AMR_EAS_EUR_poplist.ind poplistname: AMR_EAS.EIGEN.list fstonly: YES fstdetailsname: FSTdetails.out phylipoutname: FSTmatrix.phy Output: Fst statistics between populations: fst fstjack std error Z snpnumber F_st AMR EAS 0.004445 0.004445 0.000254 17.467 3595170 — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.

[TaniaPGue]

Thank you so much! I tried that, but it still outputs the summarized FST to fstdetails. I checked the log file, which with the fstonly: NO, prints the eigenvalues but the FST statistics are the same as with using fstonly: YES i.e., still not by SNP. Thank you again, for any further ideas.
This is the section in the log file that is about FST:
population: 0 AMR 463
population: 1 EAS 464
number of blocks for block jackknife: 32

end of Fst statistics between populations

fst *1000:
A E
A 0 6
E 6 0

std. err. * 1000000:
A E
A 0 294
E 294 0

[bumblenick]

I'm stuck ; I tested fstdetailsname: (which I rarely use) and it worked fine. I will soon put out a new release of smartpca on github and please then try again. Nick

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On Thu, Apr 4, 2024 at 10:55 AM Tania Guerrero ***@***.***> wrote: Thank you so much! I tried that, but it still outputs the summarized FST to fstdetails. I checked the log file, which with the fstonly: NO, prints the eigenvalues but the FST statistics are the same as with using fstonly: YES i.e., still not by SNP. Thank you again, for any further ideas. This is the section in the log file that is about FST: population: 0 AMR 463 population: 1 EAS 464 number of blocks for block jackknife: 32 end of Fst statistics between populations fst *1000: A E A 0 6 E 6 0 std. err. * 1000000: A E A 0 294 E 294 0 — Reply to this email directly, view it on GitHub <#102 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEE77B3KX5XK475FY36LF73Y3VSUXAVCNFSM6AAAAABFWE65OWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZXGQZTMMJTGY> . You are receiving this because you commented.Message ID: ***@***.***>

[TaniaPGue]

We both are. Thank you so much for your help! I'll be on the lookout for the new release :)