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I'm trying to run ADMIXTURE on some files I've generated using the Stacks pipeline. ADMIXTURE accepts .bed and .ped files, but when I try to pass the .ped file generated by Stacks to ADMIXTURE (v1.3.0), I get a "PLINK Input file error". I've pasted the head of my (tab separated) .ped file below.

head populations.plink.ped -n 1

garden QUAC_G_SH_Q1485 0 0 0 0 0 0 T T C C G G T T C C C C G G T

Alternatively, I could convert my .ped file to .bed using plink, and try to pass this to ADMIXTURE--but Stacks didn't provide me with a map file to do this, so I don't think that will work.

If anyone knows what needs to change with my .ped file (remove sample name? population designation?), I'd appreciate any tips. This is my first time running most of these programs.

Thanks!

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    $\begingroup$ Did you obtain a solution to this? I am currently facing the same issue. Thanks $\endgroup$
    – Abosede Olarewaju
    Commented May 31, 2023 at 12:52
  • $\begingroup$ @AbosedeOlarewaju this would be a good question to ask, and include some specifics of your project. $\endgroup$
    – M__ ♦
    Commented May 31, 2023 at 15:38

1 Answer 1

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Admixture requires a '12'-coded .ped file, rather than the allele-coding you're using. 'plink --file [file prefix] --recode 12' produced a .ped file that Admixture could use for me.

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