PLINK: Whole genome data analysis toolset
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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
...
where
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
plink-impute.ped
plink-impute.map
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 haplotypesTODO 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.
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