Formatting genepop output for further conversions

[alp...@ncsu.edu]

Hi everyone,

I have processed reads from my GBS double digest from ustacks up to the population step to get an output file in genepop's format. At this point I would just like to establish a way to get my data to feed into Arlequin, but I am having trouble with the file converter option in genepop. When I feed the STACKS genepop output into a windows or linux compiled versions, I get a warning like this:

Genepop version 4.2.1


Name of the data file ? (press ENTER to quit)
batch1genepop.txt
Current input file: batch1genepop.txt
(!) Invalid information for some individual: some information was found
   after all genotypes have been read for an individual.
   Check individual 1 in population 1   Suspect information: '0000    0000    0000'

Using the Genepop's website application yields another input error where the matrix looks slightly off and there are a few '!' interspersed in the file. The program also tells me how many loci IDs there are and alerts me that the matrix itself does not comply. When I inspect my original file, I see no problems according to my reading of the STACKS or genepop manual. From what I understand, it is recommended to setup a whitelist so genepop can handle NGS size files, but I want to just make sure that I have not overlooked a simple mistake? For reference, a snippet of my genepop matrix is attached. Other than changing the title of my file, the output is just as I got it from a STACKS analysis with the following parameters: populations -P ./stacks/ -M popmap.txt -b 1 -k -p 6 -r 0.5 -t 36 ‒genepop

Is there any modification that can be made to correctly feed my output into the genepop program? I am very appreciative of any help you can provide. I am new to this process and would like to optimize the quality of results once I have made it to some more downstream analyses.

Sincerely,
Andrew

[alp...@ncsu.edu]

Nevermind, I think I solved the problem. For some reason the last three loci were not divided by commas while the others were. I just wanted to share this in case there is a bug in how genepop formatted files are produced in Stacks.

Sincerely,
Andrew

[alp...@ncsu.edu]

The problem is fixed. I can now convert files in genepop.

[Julian Catchen]

Thanks, Andrew, I'll have a look at the code and make sure there is
nothing strange happening. Can you post a few more details on what the
formatting problem in the file was, perhaps post a piece of the file
that is incorrect? And, if possible, can you make sure that you didn't
modify it somehow, that is, perhaps export a fresh file and check that
it still has the problems?

Best,

julian

[Flavia Termignoni]

Thanks a lot for your post!! I had the same format problem in the STACKS output (Genepop).... Fixed !!!