New Fugue

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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 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

Estimate maximum likelihood allele frequencies
Estimate maximum likelihood haplotype frequencies

Linkage Disequilibrium Estimates

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

include marker numbers (e.g. 1, 2, 3, ...)
include marker names (e.g., rs1, rs2, rs3, ...)
include marker positions
indicate direction of association
only record markers that have rsq greater than a specific threshold

X Chromosome Analyses

Use the new_fugueX executable.


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


Abecasis GR and Wigginton JE (2005). Handling marker-marker linkage disequilibrium: pedigree analysis with clustered markers. Am J Hum Genet 77:754-67