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| [[Category:Software]] | | [[Category:Software]] |
| '''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 |
| + | |
| + | |
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| == Download == | | == Download == |