CnD: A copy number variant caller for inbred strains

cnD is a program to detect copy number variants from short read sequence data.

The target organism is assumed to be inbred, and therefore homozygous, so regions of apparent heterozygous SNPs (as called by MAQ) can be used to detect copy number gains. cnD uses both the rate of these paralogous sequence variants, and the raw sequence depth, to call copy number gains and losses using a hidden markov model.

[Genome Research Limited]

Publications

  • Copy number variant detection in inbred strains from short read sequence data.

    Simpson JT, McIntyre RE, Adams DJ and Durbin R

    Bioinformatics (Oxford, England) 2010;26;4;565-7

* quick link - http://q.sanger.ac.uk/czfrdlz5