PLINK: Whole genome data analysis toolset [an error occurred while processing this directive]
Multimarker haplotype tests
All tests described above are based on single SNP tests. It is also possible to impute haplotypes based on multimarker predictors using the standard E-M algorithm and to create a new file with the most likely haplotype pair imputed (or set to missing if the most likely phase is below a certain value).

Soon to be added: the ability to perform the test of association on the posterior distribution of haplotypes given genotypes for each individual (for main disease and quantitative trait population-based association tests only).
Imputing multimarker haplotypes

The command

plink --file mydata --tag mytagfile

will read the mytagfile, which is expected to be in format:
     rs1001 5 0 201  1 2   T     snp1
     rs1002 5 0 202  A C   TTA   snp1 snp3 snp4
     Col 1 : Imputed SNP name
     Col 2 : Imputed SNP chromosome
     Col 3 : Imputed SNP genetic distance (default: Morgan coding)
     Col 4 : Imputed SNP physical position (bp units)
     Col 5 : Imputed SNP allele 1 name
     Col 6 : Imputed SNP allele 2 name
     Col 7 : Tag SNP allele/haplotype that equals imputed SNP allele 1
     Col 8+ : Tag SNP(s) [in same order as haplotype in Col 7]
and create two new files
based on the E-M phase reconstructed haplotypes.

This option is under construction To perform haplotype-based tests, two steps are involved: imputing these haplotypes, then testing the new file, as though the imputed haplotypes were SNPs that you have directly observed. The imputed haplotype file can be merged with the original SNP file with the --merge option.

Imputing multimarker haplotypes

TODO Soon to be added: tests that account for the potential ambiguous phase reconstruction (i.e. to fractionally count haplotypes). The package whap already performs such an analysis, but it is not ideally suited to very large-scale analysis.

[an error occurred while processing this directive]
This document last modified [an error occurred while processing this directive]