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Open Access Highly Accessed Methodology article

Fast detection of de novo copy number variants from SNP arrays for case-parent trios

Robert B Scharpf1*, Terri H Beaty2, Holger Schwender3, Samuel G Younkin5, Alan F Scott4 and Ingo Ruczinski5

Author Affiliations

1 Department of Oncology, Johns Hopkins University, Baltimore, MD, USA

2 Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA

3 Mathematical Institute, Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany

4 Department of Medicine, Johns Hopkins University, Baltimore, MD, USA

5 Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA

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BMC Bioinformatics 2012, 13:330  doi:10.1186/1471-2105-13-330

Published: 12 December 2012

Additional files

Additional file 1:

Optional post-processing of CBS segments. Removing splits from CBS as a function of coverage and the standardized difference in segment means. Baum-welch updates Initialization and updating of parameters for the emission distributions. Models for Mendelian transmission of the offspring copy number Details regarding the adaption of the PennCNV probabilistic model of Mendelian transmission. PennCNV annotation for trio copy number states Annotation of trio copy number states in PennCNV. Empirical estimation of simulation parameters in the oral cleft study Estimation of simulation parameters from the oral cleft study Renvironment and software versions

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Additional file 2:

Supplementary figures. Supporting figures.

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Open Data