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PMID: 24172663 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

EXCAVATOR: detecting copy number variants from whole-exome sequencing data.

Genome biology ·Vol. 14 ·No. 10 ·2013-00-00 ·Pages R120

Magi A, Tattini L, Cifola I, D'Aurizio R, Benelli M, Mangano E, Battaglia C, Bonora E, Kurg A, Seri M, Magini P, Giusti B, Romeo G, Pippucci T, De Bellis G, Abbate R, Gensini GF

Abstract

We developed a novel software tool, EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies genomic regions into five copy number states. We validate EXCAVATOR on three datasets and compare the results with three other methods. These analyses show that EXCAVATOR outperforms the other methods and is therefore a valuable tool for the investigation of CNVs in largescale projects, as well as in clinical research and diagnostics. EXCAVATOR is freely available at http://sourceforge.net/projects/excavatortool/.

MeSH Terms
Algorithms Computational Biology/methods DNA Copy Number Variations Exome Genome Genomics High-Throughput Nucleotide Sequencing Humans Intellectual Disability/genetics Markov Chains Melanoma/genetics,pathology Polymorphism, Single Nucleotide ROC Curve Reproducibility of Results Software
Authors & Affiliations
17 authors, click to expand affiliations / ORCID
Magi Alberto
Tattini Lorenzo
Cifola Ingrid
D'Aurizio Romina
Benelli Matteo
Mangano Eleonora
Battaglia Cristina
Bonora Elena
Kurg Ants
Seri Marco
Magini Pamela
Giusti Betti
Romeo Giovanni
Pippucci Tommaso
De Bellis Gianluca
Abbate Rosanna
Gensini Gian Franco
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/gb-2013-14-10-r120
Published
2013-00-00
Pages
R120
Language
English
Region
England
NLM ID
100960660
PMCID
PMC4053953
Subset
IM
External Links
PubMed source DOI: 10.1186/gb-2013-14-10-r120 PMC Full Text View journal details
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