CnD
Application data |
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Biological application domain(s) | Copy number estimation |
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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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