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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 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
