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, 13:35, 27 September 2010
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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]. |
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− | == Command Line Options ==
| + | = Command Line Options = |
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− | === Input Files ===
| + | == Input Files == |
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| ; -d ''datafile'' | | ; -d ''datafile'' |
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| : Output file prefix. | | : Output file prefix. |
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− | === Frequency Estimates ===
| + | == Frequency Estimates == |
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| ; --alleles | | ; --alleles |
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| : Estimate maximum likelihood haplotype frequencies | | : Estimate maximum likelihood haplotype frequencies |
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− | === Linkage Disequilibrium Estimates ===
| + | == Linkage Disequilibrium Estimates == |
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| ; --diseq | | ; --diseq |
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| : Only report linkage disequilibrium for marker pairs that include ''marker'' | | : Only report linkage disequilibrium for marker pairs that include ''marker'' |
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− | === Linkage Disequilibrium File Options ===
| + | == Linkage Disequilibrium File Options == |
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| ; --ids | | ; --ids |
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| : only record markers that have rsq greater than a specific threshold | | : only record markers that have rsq greater than a specific threshold |
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| + | == X Chromosome Analyses == |
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| + | Use the <code>new_fugueX</code> executable. |
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| == Download == | | == Download == |
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− | A source file with the current distribution is available for download from this [http://www.sph.umich.edu/csg/abecasis/downloads/generic-new_fugue-2010-05-25.tar.gz source tar-ball]. | + | 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: |
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| + | tar -zxvf generic-new_fugue-2010-06-02.tar.gz |
| + | cd generic-new_fugue |
| + | make all |
| + | make install |
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| + | 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 |
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| == References == | | == References == |
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| 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 |