Difference between revisions of "New Fugue"
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== Download == | == Download == | ||
− | A source file with the current distribution is available for download from this [http://www.sph.umich.edu/csg/abecasis/downloads/generic-new_fugue-2010- | + | A source file with the current distribution is available for download from this [http://www.sph.umich.edu/csg/abecasis/downloads/generic-new_fugue-2010-06-02.tar.gz source tar-ball]. |
== References == | == References == | ||
Abecasis GR and Wigginton JE (2005). Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. Am J Hum Genet 77:754-67 | Abecasis GR and Wigginton JE (2005). Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. Am J Hum Genet 77:754-67 |
Revision as of 13:22, 2 June 2010
New Fugue is a program for estimation of haplotype frequencies and linkage disequilibrium coefficients in family data. The current implementation uses the methods described by Abecasis and Wigginton (2005) and originally implemented in the Merlin package.
Command Line Options
Input Files
- -d datafile
- Data file in Merlin format. Only marker fields will be considered.
- -p pedigreefile
- Pedigree file in Merlin format.
- -m mapfile
- Map file in Merlin format.
- -o prefix
- Output file prefix.
Frequency Estimates
- --alleles
- Estimate maximum likelihood allele frequencies
- --haplotype
- Estimate maximum likelihood haplotype frequencies
Linkage Disequilibrium Estimates
- --diseq
- Calculate pairwise linkage disequilibrium, results will be stored in a .xt file.
- --maf minmaf
- Only calculate pairwise disequilibrium for SNPs with minor allele frequency of minmaf or greater.
- --window basepairs
- Only calculate pairwise disequilibrium estimates for SNPs with basepairs of each other.
- --sample fraction
- Sample a fraction of marker pairs for which to report linkage disequilibrium.
- --pairWith marker
- Only report linkage disequilibrium for marker pairs that include marker
Linkage Disequilibrium File Options
- --ids
- include marker numbers (e.g. 1, 2, 3, ...)
- --names
- include marker names (e.g., rs1, rs2, rs3, ...)
- --positions
- include marker positions
- --coupling
- indicate direction of association
- --minrsq
- only record markers that have rsq greater than a specific threshold
X Chromosome Analyses
Use the new_fugueX
executable.
Download
A source file with the current distribution is available for download from this source tar-ball.
References
Abecasis GR and Wigginton JE (2005). Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. Am J Hum Genet 77:754-67