Hi,

This is regarding a problem that I am facing with testing whether SNPs have independent effect using Plink. We have sequencing information of a gene with 10kb upsteam from ATG and all exons. I was testing for independent effect of each of my associated SNPs using plink with a quantitative trait with interval with first and last SNP. How ever It returned an error such as ERROR: Could not fit conditional haplotype models: collinearity issues from a badly-specified model. Any suggestions on sorting it out are welcome

Regards
Toyanji Joseph