Hello,
I have ddRAD data for 8 populations (48 samples in total) and looking for resistance lined SNP in one of the population. I did run data on Stacks and got the final outputs which included vcf file. Right now my question is that do I need to process the output of Stacks with another software? If not how I can interpret the output of Stacks?
Thanks!
Mahnaz,
Depending on your analysis, you need to export your data to a file type that can be read by a program, like Structure to look for the presence of distinct populations, admixed individuals or allele frequencies.
If you look at the Stacks manual, it has some additional information. Then search for Structure genetics, look at it's intended use for studying populations.
Thank you Paul for giving me clue, I already got the Structure output from the Stacks and I will check the Structure manual.
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