title: EXCAVATOR: detecting copy number variants from whole-exome sequencing data.
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/.
authors.forename: Alberto
authors.initials: A
authors.lastname: Magi
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Tattini
authors.forename: Ingrid
authors.initials: I
authors.lastname: Cifola
authors.forename: Romina
authors.initials: R
authors.lastname: D'Aurizio
authors.forename: Matteo
authors.initials: M
authors.lastname: Benelli
authors.forename: Eleonora
authors.initials: E
authors.lastname: Mangano
authors.forename: Cristina
authors.initials: C
authors.lastname: Battaglia
authors.forename: Elena
authors.initials: E
authors.lastname: Bonora
authors.forename: Ants
authors.initials: A
authors.lastname: Kurg
authors.forename: Marco
authors.initials: M
authors.lastname: Seri
authors.forename: Pamela
authors.initials: P
authors.lastname: Magini
authors.forename: Betti
authors.initials: B
authors.lastname: Giusti
authors.forename: Giovanni
authors.initials: G
authors.lastname: Romeo
authors.forename: Tommaso
authors.initials: T
authors.lastname: Pippucci
authors.forename: Gianluca
authors.initials: G
authors.lastname: De Bellis
authors.forename: Rosanna
authors.initials: R
authors.lastname: Abbate
authors.forename: Gian Franco
authors.initials: GF
authors.lastname: Gensini
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D056915:DNA Copy Number Variations; D059472:Exome; D016678:Genome; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008607:Intellectual Disability / Q000235:genetics; D008390:Markov Chains; D008545:Melanoma / Q000235:genetics / Q000473:pathology; D020641:Polymorphism, Single Nucleotide; D012372:ROC Curve; D015203:Reproducibility of Results; D012984:Software