Input files for whole-genome scans.

[javibio-git]

Hi

I am interested in using this package to calculate α using my SNP data (VCF files) for Drosophila. As far as I can tell, the input should be d0 and d and a file containing the DAF and polymorphism data (synonymous and nonsynonymous). However, I am not sure how exactly I should calculate the values for d0 and d. It is not clear what should I use as a neutral reference region.

In addition, I was looking at the provided example file (x,pN,pS) and I am not sure what each row is representing. Is each row a population, gene or maybe a region?

Not sure if this is still maintained but if someone see this, any clarification on the above would be much appreciated.

Thank you

Javier,

[bhaller]

It is maintained, yes. :-> @philippmesser can you field this?