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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
== Download ==
== Download ==
