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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]. | + | [[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]. |
| + | |
| + | = 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 <code>new_fugueX</code> executable. |
| | | |
| == Download == | | == Download == |
| | | |
− | A source file with the current distribution is available for download from this link: [http://www.sph.umich.edu/csg/abecasis/downloads/generic-new_fugue-2010-05-11.tar.gz generic-new_fugue-2010-05-11.tar.gz]. | + | 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]. After downloading, you should unpack the archive using <code>tar</code> and run <code>make</code> to compile and install <code>new_fugue</code>. Typically, that should work like this: |
| + | |
| + | tar -zxvf generic-new_fugue-2010-06-02.tar.gz |
| + | cd generic-new_fugue |
| + | make all |
| + | make install |
| + | |
| + | In some systems, notably those based on Ubuntu, you might see an error message complaining that zlib is missing. [[zlib]] is required for |
| + | new_fugue to handle compressed files. If you have administrative privileges on your machine, you will want to install zlib using the <code>yum</code> package manager. The command line will look like this: |
| + | |
| + | yum install zlib-devel |
| + | |
| + | If yum is not installed, you can try the following: |
| + | |
| + | sudo apt-get install zlib1g-dev |
| | | |
| == 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 |