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
- -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.
- 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
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