Population information added to populations.snps.vcf

[Justin Chandler-Holtz]

Hello everyone,

This is my first time working with stacks and genomic data, and I have arrived at a bit of an impasse with my project.  I need to make a PCA (which I have figured out how to do) with my populations.snps.vcf file (which I have set to ---write-single-snp), however, the populations.snps.vcf file does not have population information for each sample in it, despite using a poplog to run the populations function of stacks.

Is there a way to generate a populations.snps.vcf file with the populations function of stacks that contains populations information?

Thanks
  - Justin

[Catchen, Julian]

Hi Justin,

 

I am not aware of a method to encode population information into VCF files, that is, the format does not provide for this information as far as I know (but send an example if you have one). Most people doing PCA on RADseq data with Stacks will export a GenePop file and import it into Adegenet (https://catchenlab.life.illinois.edu/stacks/manual/#export). Both the GenePop and Structure outputs encode population information (using different, format-specific methods).

 

I’m also not sure what you mean by ‘poplog’, do you mean ‘population map’?

 

Best,

Julian