Plink to Treemix

Question

[dirranrak]

Hi all,

I tried to convert Plink file to Treemix file, I remarked that in the note at different websites you need to get a .frq file from using --freq --within flag in Plink. But the thing is that when you use the these flags in the same run, you get a .frq.strat file but not only .frq. I followed the way to create the .clust or .txt file for using --within flag. I checked the the .frq.strat file and I saw that most of individuals in most of the populations do not have allele frequency (just 0). I continued to gzip the file and use it with the Plinktotreemix.py. I did run the file with Treemix, the gziped file was just 38 bytes and th run was aborted, It said that "Ind: 0, SNP: 0".

The cluster file is just a file with three columns: 1: FID, 2: IID, 3: FID (I considered the FID which is the population as group). These three columns have the same number of row.

What should be the problem? Could anyone help?

Thanks a lot

[Gabriel R.]

I am not sure about your problem but you could import your plink file into glactools, do the filtering and export to treemix.

Answer 1

[strive]

You can try this method