sweepfinder2

Question

[sevda]

Hello, I am trying to use sweepfinder2 software but I do not know how can I get B-value file as an input data. Can i creat that by just vcf file? Regards, Sevda

Answer 1

[Trivas]

From the Sweepfinder2 publication:

B-values range from 0 to 1 and are proportional to local reductions in genetic diversity or effective population size due to background selection. McVicker et al. (2009) provide a method for inferring B-values using comparative data, thereby providing an opportunity for separating background selection from the effect of selective sweeps inferred from within-population polymorphism data.

McVicker 2009: https://journals.plos.org/plosgenetics/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000471

You'll have to read the methods section in that paper and do some lifting on your own. Or email the authors of Sweepfinder2.

[sevda]

Thank you for your guide, I could run sweepfinder2 by this command "SweepFinder2 –lg g". but in result ,I got location, LR and alpha amount but how can I get CLR and start and end positions too.