Investigators:
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Andy Rimmer, Katherine Bull
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Description
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LGENU is a program designed to infer ancestral haplotypes in ENU-mutated mice, from next-generation SNP calls, using the Lander-Green algorithm.
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Capabilities
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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.
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Reference:
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A manuscript describing this method is currently being prepared for publication.
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Resources:
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You can download the latest stable version of LGENU here.
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Contact:
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Bug reports, comments, and feature requests can be sent to Andy Rimmer
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