CnD

Application data
Biological application domain(s)	Copy number estimation
Principal bioinformatics method(s)
Created at	Wellcome Trust Sanger Institute
Maintained?	Maybe
Programming language(s)	D
Licence	GPL

Summary: Program to detect copy number variation in inbred mouse strains

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We have developed an algorithm to detect copy number variants (CNVs) in homozygous organisms, such as inbred laboratory strains of mice, from short read sequence data. Our novel approach exploits the fact that inbred mice are homozygous at virtually every position in the genome to detect CNVs using a hidden Markov model (HMM). This HMM uses both the density of sequence reads mapped to the genome, and the rate of apparent heterozygous single nucleotide polymorphisms (SNP), to determine genomic copy number.

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References

1. . 2010. Bioinformatics

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