pairwise fst between all populations in plink2

[s m]

Hi,

I am using PLINK v2.00a3LM AVX2 Intel and I would like to calculate global pairwise fst between all sets of populations.

I have a set of .bim .bed and .fam which contains individuals from different populations. I also have a .pheno file which each line for an individual and the second column with the population id, e.g.:

#IID pop
Ami_Coriell_NA13615 Ami_Coriell
Ami_Coriell_NA13616 Ami_Coriell
Armenian_armenia86 Armenian_Armenian
Armenian_armenia91 Armenian_Armenian
Armenian_armenia102 Armenian_Armenian

I've run the command:

plink2 \
    --bfile /cluster/project8/hellenthal/SamMorris/analysis/data_projects/modern/Africa/genotypedData/allAncients.africanReference.withFan.AllChr.PHASED2.highAccuracySNPs.pruned \
    --fst pop \
    --pheno /cluster/project8/hellenthal/SamMorris/analysis/data_projects/modern/Africa/genotypedData/allAncients.africanReference.withFan.AllChr.PHASED2.highAccuracySNPs.pruned.pheno

which returns:

>     --bfile /cluster/project8/hellenthal/SamMorris/analysis/data_projects/modern/Africa/genotypedData/allAncients.africanReference.withFan.AllChr.PHASED2.highAccuracySNPs.pruned \
>     --fst pop \
>     --pheno /cluster/project8/hellenthal/SamMorris/analysis/data_projects/modern/Africa/genotypedData/allAncients.africanReference.withFan.AllChr.PHASED2.highAccuracySNPs.pruned.pheno
PLINK v2.00a3LM AVX2 Intel (23 Sep 2020)       www.cog-genomics.org/plink/2.0/
(C) 2005-2020 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to plink2.log.
Options in effect:
  --bfile /cluster/project8/hellenthal/SamMorris/analysis/data_projects/modern/Africa/genotypedData/allAncients.africanReference.withFan.AllChr.PHASED2.highAccuracySNPs.pruned
  --fst pop
  --pheno /cluster/project8/hellenthal/SamMorris/analysis/data_projects/modern/Africa/genotypedData/allAncients.africanReference.withFan.AllChr.PHASED2.highAccuracySNPs.pruned.pheno

Start time: Thu Oct 15 10:59:39 2020
128648 MiB RAM detected; reserving 64324 MiB for main workspace.
Allocated 8586 MiB successfully, after larger attempt(s) failed.
Using up to 20 threads (change this with --threads).
6343 samples (0 females, 0 males, 6343 ambiguous; 6343 founders) loaded from
/cluster/project8/hellenthal/SamMorris/analysis/data_projects/modern/Africa/genotypedData/allAncients.africanReference.withFan.AllChr.PHASED2.highAccuracySNPs.pruned.fam.
250846 variants loaded from
/cluster/project8/hellenthal/SamMorris/analysis/data_projects/modern/Africa/genotypedData/allAncients.africanReference.withFan.AllChr.PHASED2.highAccuracySNPs.pruned.bim.
2 categorical phenotypes loaded.
End time: Thu Oct 15 10:59:39 2020

However, I have many more than 2 (~200) populations, rather than the 2 detailed in the output. I think this is the wrong way to do it, but I am not sure which is the correct way. I think I am probably specifying the phenotype (population) / file incorrectly. Could you suggest the best way to do this. Thank you.

[Christopher Chang]

Actually, the problem is that I forgot to insert a "--fst is under development" error message.  I'll post again in this thread when --fst is available.

[Christopher Chang]

--fst's Hudson method is now implemented.

On Thursday, October 15, 2020 at 3:06:07 AM UTC-7 samcm...@gmail.com wrote:

[Muhammad Moaeen-ud-Din]

Command to run it please as I tried following command but no result

./plink2 --cow --bfile blackhwe --fst's Hudson method case-control --within plink.clst --out fst2

it returns nothing

[Christopher Chang]

Please read the --fst documentation.