LOSITAN only recognising one loci from STACKS genepop file

Question

[jamierobertsells]

Hi all,

I'm trying to analyse SNP data created within STACKS and out put from STACKS within genepop format for Lositan. When I import the data, Lositan only seems to identify 1 loci, and in fact this almost seems to be the header information in the genpop file. I created the genpop file on Linux for use on a windows machine and have tried running the file as straight output, and also a unix 2 dos conversion, but still only 1 locus of 600 is reocgnised. Any thoughts?

Many thanks

Jamie

[cordeiro.emg]

Hi Jamie. I have the same problem here. Did you find a solution for that problem? It was already a nightmare to install this program and now this...

Answer 1

[a.r.hoelzel]

Sorry for the late answer - only just saw this. The list of loci in your genepop input file needs to be vertical, not horizontal. You can convert this using PGDspider (just convert from genepop to genepop).