Question: VCF file conversion to BayeScan format is not working
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gravatar for lleipnitz
5 months ago by
lleipnitz0
lleipnitz0 wrote:

Hello all!

I am currently having trouble to convert a .vcf file to a bayescan input that takes into account the population information. I have a dataset of 34 individuals divided into 10 populations and over 34K SNPs to analyze. I have tried converting a .vcf file (generated through the STACKS program) to a bayescan input file using PDGspider. Unfortunately, while the conversion is successful, PDGspider seems to ignore the population information I have provided in the SPID file (e.g. a simple text file containing two columns, one with individual information and another with population information). The conversion generates a file considering a single population only, and - apparently - does not distinguish individual information.

I am assuming I have the wrong idea about how to make a population info file or I could be missing some necessary steps in between the VCF -> Bayescan conversion. I have seen other posts here and elsewhere ( I do not remember if it was on ResearchGate or google groups) suggesting A three-step conversion, like VCF -> PGD -> bayescan, but it did not work for me.

Any thoughts? Help would be greatly appreciated!

Very best, Leonardo.

ADD COMMENTlink modified 5 months ago by Biostar ♦♦ 20 • written 5 months ago by lleipnitz0
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