Joint with Alejandro Cáceres (ISGlobal), we have developed a method that can be applied to common GWAS for calling the inversion genotypes, which accounts for population stratification when an appropriate reference population is not known. This method is extremely useful when performing inversion association studies in a GWAS context were population stratification can be present.
To install `invClust`, start R and enter:
“`
source(“http://www.creal.cat/media/upload/arxius/jr/CREAL_install/install.R”)
creal.install(“invClust”)
“`
If you experiment some problem during this process, the source code of the package can be download from [here](http://www.creal.cat/media/upload/arxius/jr/inversions/invClust_1.0.tar.gz).
The methods are described in the manuscript:
> *Cáceres and González, J. R. (2015) Following the footprints of polymorphic inversions on SNP data: from detection to association tests. NAR doi:10.1093.*