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

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[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

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

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[TaniaPGue]

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