I am attempting to run GCTA for a chromosome partitioning study using related individuals. I am using the new GCTA version with the Zaitlen et al. (2013 PLoS Genetics) method.
However, when I try to run a chromosome partition analysis I get the error: "the information matrix is not invertible". I am fitting all chromosomes in the model using the 2 GRMs (from all SNPs in a family data set and the additional GRM using --make-bK 0.05)
Does this new method allow for the estimation of variance explained by each chromosome?
I would not use this method for a genome partitioning analysis because the variance of GRM for a single chromosome is much larger than that for the whole genome so that that a threshold of 0.05 is no longer applied.