Changes

'''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 ==

= Command Line Options =

=== Input Files ===

== Input Files ==

; -d ''datafile''

; -d ''datafile''

: Output file prefix.

: Output file prefix.

=== Frequency Estimates ===

== Frequency Estimates ==

; --alleles

; --alleles

: Estimate maximum likelihood haplotype frequencies

: Estimate maximum likelihood haplotype frequencies

=== Linkage Disequilibrium Estimates ===

== Linkage Disequilibrium Estimates ==

; --diseq

; --diseq

: Only report linkage disequilibrium for marker pairs that include ''marker''

: Only report linkage disequilibrium for marker pairs that include ''marker''

=== Linkage Disequilibrium File Options ===

== Linkage Disequilibrium File Options ==

; --ids

; --ids

; --minrsq

; --minrsq

: only record markers that have rsq greater than a specific threshold

: only record markers that have rsq greater than a specific threshold

== Download ==

== Download ==