Version

2.0, installed in HIPPU

Description

DHSMAP is a program for fine-mapping of qualitative traits based on linkage disequilibrium. The program implements the Decay of Haplotype Sharing method, originally published by McPeek and Strahs in 1999. The program uses a maximum-likelihood or maximum quasi-likelihood model to estimate the gene location, and uses Markov models to take background linkage disequilibrium into account. The program utilizes either haplotype or genotype data.

DHSMAP can be used for obtaining:

1. estimates of the location of the trait-associating gene with the corresponding likelihood surface and the 95% confidence intervals

2. estimates of the ancestral haplotypes

3. the expected lengths of the conserved ancestral segments

4. the proportions of haplotypes descended from the ancestors

Usage

DHSMAP program is installed on  HIPPU (hippu.csc.fi).

The program needs to be initialized before use:

module load dhsmap

DHSMAP needs two input files, datafile and pedfile. The file formats are described in the manual.

To run DHSMAP type (in this example the datafile is caled "data.in" and the pedfile "ped.in"):

dhsmap data.in ped.in

Upon successful execution, the program generates four output files:

• resout: the point estimates and 95% confidence intervals for the gene location

• ancout: the sets of ancestral haplotypes estimated in different stages of the procedure

• maxout: parameter estimates and diagnostic statistics corresponding to the estimated ancestral haplotypes

• oneout: estimates of the gene location on a fine grid, given the set of ancestral haplotypes estimated before.

For a full description of the output, refer to the output section of the manual.

Documentation

Detailed description about file formats, algorithms, and interpretation of results are available in the DHSMAP manual.

References

McPeek MS, Strahs A (1999) Assessment of linkage disequilibrium by the decay of haplotype sharing, with application to fine-scale genetic mapping, American Journal of Human Genetics 65:858-875.

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