haplotype association analysis with plink

[Carlo Maj]

Dear all,

I performed an imputation withe the pipeline SHAPEIT-> Minimac3 by first estimate the haplotype of the gwas input data with respect to 1Kgenome data.

I therefore obtained the haps/sample haplotype files which I used for the following imputation.

I wonder if there is a way to perform haplotype association analysis (instead of single variant association analysis) by using the haplotype information of haps/sample files in plink2?

Best,

Carlo

[Christopher Chang]

This isn't yet possible with plink2.  However, a simple Python library for working with .haps+.sample data (converted to plink 2.0 format) will be available within a few days.