Difference between revisions of "New Fugue"
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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 | ||
+ | |||
+ | == 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 | + | 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 |
Latest revision as of 13:35, 27 September 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. After downloading, you should unpack the archive using tar
and run make
to compile and install new_fugue
. 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 yum
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
Abecasis GR and Wigginton JE (2005). Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. Am J Hum Genet 77:754-67