Difference between revisions of "New Fugue"
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'''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 [http://www.sph.umich.edu/csg/abecasis/Merlin Merlin package]. | '''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 [http://www.sph.umich.edu/csg/abecasis/Merlin 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 | ||
+ | |||
+ | |||
== Download == | == Download == |
Revision as of 11:04, 25 May 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
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