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EXCAVATOR

A read count based tool that exploits all the reads produced by whole-exome sequencing (WES) experiments to detect copy Number Variants (CNVs) with a genome-wide resolution. EXCAVATOR2 enhances the identification of genomic CNVs (overlapping or non-overlapping exons) from WES data by integrating the analysis of In-targets and Off-targets reads. It extends the RC approach to the whole genome sequence and exploits the shifting level model (SLM) algorithm to segment the two combined profiles. Thereafter, the FastCall algorithm allows to classify each segmented region into five possible states (two-copy deletion, one-copy deletion, normal, one-copy duplication and multiple-copy amplification).

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EXCAVATOR forum

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EXCAVATOR classification

EXCAVATOR specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
Perl
Version:
2.0
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable

EXCAVATOR distribution

versioning

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No versioning.

EXCAVATOR support

Documentation

Maintainer

  • Romi D'Aurizio <>

Credits

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Publications

Institution(s)

Laboratory of Integrative Systems Medicine (LISM), Institute of Informatics and Telematics and Institute of Clinical Physiology, National Research Council, Pisa, Italy; Medical Genetics Unit, Sant'Orsola Malpighi Polyclinic, Bologna, Italy; Department of Computer Science, University of Pisa, Pisa, Italy; Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy

Funding source(s)

Flagship project InterOmics (PB. P05, CUP B91J12000270001), Italian Ministry for Instruction University and Research (MIUR) and CNR organisations; Italian Ministry of Health, Young Investigators Award for the Project GR-2011-02352026 ‘Detecting copy number variants from whole-exome sequencing data applied to acute myeloid leukemias’

Link to literature

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