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Control-FREEC

A tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data. Control-FREEC automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. The control (matched normal) sample is optional. The program can also use mappability data (files created by GEM).

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Control-FREEC classification

Control-FREEC specifications

Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux, Windows
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Input format:
SAM, BAM, Pileup, Eland, BED, SOAP, arachne, BLAT, Bowtie
Programming languages:
C++, R
Stability:
Stable

Control-FREEC distribution

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Control-FREEC support

Documentation

Credits

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Publications

Institution(s)

Institut Curie, Paris, France, INSERM, U900, Bioinformatics and Computational Systems Biology of Cancer, Paris, France; Mines ParisTech, Fontainebleau, France; INSERM, U830, Genetics and Biology of Cancers, Paris, France; INRIA Saclay, Orsay, France

Funding source(s)

This work was supported by the ‘Projet Incitatif et Collaboratif Bioinformatique et Biostatistiques’ of the Institut Curie; Ligue Nationale Contre le Cancer.

Link to literature

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