A full tutorial is under construction. The README file (pasted below), should get you started.

README File

WHaIT, Weighted Haplotype and Imputation-based Tests, are tests for association of multiple rare variants with binary traits. It consists of two tests:

(1) Weighted Haplotype test and 
(2) Weighted Imputation Dosage test.

To perform test (1) Weighted Haplotype test:

    Input files: caes haplotypes and control haplotypes. Each line contains one haplotype, no delimiter between alleles. 

    Sample command line: 
 
        ./wh.pl -cth ../example/controls.hap -csh ../example/cases.hap
	
To perform test (2) Weighted Imputation Dosage test:

    Input files: case dosages, control dosages, and marker information in MaCH (http://www.sph.umich.edu/csg/abecasis/mach/) output format. 

                 Each line in dosage file is for one individuals with two heading columns in the format of "famid->individalID DOSAGE".
                 The heading columns are NOT used. 
                 Additional columns: one column for one marker.
                 The heading columns and dosage columns are white-space delimited.
                 
                 Each line in marker information file is for one marker. 
                 Each line contains seven fields: marker name, allele1, allele2, Freq1, MAF, Quality, and Rsq. 
                 Only the first three columns are used.
                 Columns are white-spece delimited.
                 Header line is optional.

    Sample command line:

        ./wid.pl -ctd ../example/controls.dose -csd ../example/cases.dose -info ../example/sample.info

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Other FAQ:

(*) How to install?

    (1) uncompress: 

            tar -zxvf whait.linus.tgz 

    (2) compile and copy to bin

            set binpath = ~/bin/
            #modify ~/bin/ to one of the $PATH dir
            ./build.csh $binpath

(*) Which test to choose?

    (**) If only using GWAS SNPs, weighted haplotype test is more powerful;
    (**) If additional SNPs are imputed using external reference, weighted imputation dosage test is preferred.