Hello everyone,
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!
