LGENU

Investigators:  Andy Rimmer, Katherine Bull
   

Description

LGENU is a program designed to infer ancestral haplotypes in ENU-mutated mice, from next-generation SNP calls, using the Lander-Green algorithm.

Capabilities

The program currently works properly only for a fixed pedigree, and needs SNP data from 3 sibling mice. It takes a VCF file of SNP calls, a map of recombination rates across the mouse genome, a window size, and a value for the ENU mutation rate. The output is a text file consisting of inferred ancestral haplotypes across the genome for each moue. A test VCF file  is provided with the program.

   
Reference:  A manuscript describing this method is currently being prepared for publication.
   

Resources:

You can download the latest stable version of LGENU  here.

Contact:  Bug reports, comments, and feature requests can be sent to Andy Rimmer