ExomeCopy

Application data
Created by	Love MI
Biological application domain(s)	Exome and whole genome variant detection, Copy number estimation, Exome analysis
Principal bioinformatics method(s)
Created at	Max-Planck-Institute for Molecular Genetics
Maintained?	Yes
Input format(s)	BAM
Software features	simultaneous normalization and segmentation
Programming language(s)	R
Software libraries	Bioconductor
Licence	GPL 2.0+
Operating system(s)	Linux, Windows, Mac OS X

Summary: CNV detection from exome sequencing read depth

"Error: no local variable "counter" was set." is not a number.

Description

Detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.

Links

• ExomeCopy Homepage [ edit link ]
• ExomeCopy Publication full text [ edit link ]

• Add a Link

References

1. . 2011. Statistical Applications in Genetics and Molecular Biology

To add a reference for ExomeCopy, enter the PubMed ID in the field below and click 'Add'.

 

[ edit box ]

Search for "ExomeCopy" in the SEQanswers forum / BioStar or:

Web Search	Wiki Sites	Scientific
Google. Bioinformatics journals Clusty	WikiPedia MetaBase BioPedia OpenWetWare bifx wiki	PubMed Europe PMC ScientificCommons.org