Published October 17, 2019 | Version 1.0
Software Open

Python based parallel CNV calling prioritizing mpi4py usage and memory optimization

Authors/Creators

  • 1. CHU Sainte-Justine

Contributors

Project member:

  • 1. CHU Sainte-Justine

Description

Mind-GenesParallelCNV is freeware tool which mainly implemented to compute CNV calling parallel tasks in the most efficient method. The tool is design to make the command lines as much easier and simple as possible so that researchers form different informatics background level can integrate it in their research project. Also, It has been built to make the parallel tasks possible to be executed on any type of computer including desktops. The tools only work on linux64 for the moment. Other than focusing on calling CNV in parallel, the tool is meant to help detecting CNV using several type of callers based on different algorithms (implementation language may differ between algos). For the moment, the tool generates parallel calls from PennCNV and QuantiSNP, but other CNV caller such as IPattern, BCFtools, FastSeg, DNAcopy, etc will be implemented very soon so that better consensus results can be made available.

Files

MIND-GENESPARALLELCNV.zip

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Additional details

References

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  • Wang K, Li M, Hadley D, Liu R, Glessner J, Grant S, Hakonarson H, Bucan M. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data Genome Research 17:1665-1674, 2007
  • Diskin SJ, Li M, Hou C, Yang S, Glessner J, Hakonarson H, Bucan M, Maris JM, Wang K. Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms Nucleic Acids Research 36:e126, 2008
  • Wang K, Chen Z, Tadesse MG, Glessner J, Grant SFA, Hakonarson H, Bucan M, Li M. Modeling genetic inheritance of copy number variations Nucleic Acids Research 36:e138, 2008
  • Colella, S.,* Yau, C.,* Taylor, J.M., Mirza, G., Butler, H., Clouston, P., Basset, A.S., Seller, A., Holmes, C., and Ragoussis, J. QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Research, 35(6):2013-2025 2007