EXCAVATOR: detecting copy number variants from whole-exome sequencing data
Identifieur interne : 000449 ( Main/Exploration ); précédent : 000448; suivant : 000450EXCAVATOR: detecting copy number variants from whole-exome sequencing data
Auteurs : Alberto Magi [Italie] ; Lorenzo Tattini [Italie] ; Ingrid Cifola [Italie] ; Romina D Urizio [Italie] ; Matteo Benelli [Italie] ; Eleonora Mangano [Italie] ; Cristina Battaglia [Italie] ; Elena Bonora [Italie] ; Ants Kurg [Estonie] ; Marco Seri [Italie] ; Pamela Magini [Italie] ; Betti Giusti [Italie] ; Giovanni Romeo [Italie] ; Tommaso Pippucci [Italie] ; Gianluca De Bellis [Italie] ; Rosanna Abbate [Italie] ; Gian Franco Gensini [Italie]Source :
- Genome Biology [ 1465-6906 ] ; 2013.
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
Url:
DOI: 10.1186/gb-2013-14-10-r120
PubMed: 24172663
PubMed Central: 4053953
Affiliations:
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Le document en format XML
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<front><div type="abstract" xml:lang="en"><sec><title></title>
<p>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 <ext-link ext-link-type="uri" xlink:href="http://sourceforge.net/projects/excavatortool/">http://sourceforge.net/projects/excavatortool/</ext-link>
.</p>
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</div>
</front>
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</TEI>
<affiliations><list><country><li>Estonie</li>
<li>Italie</li>
</country>
<region><li>Lombardie</li>
<li>Toscane</li>
</region>
<settlement><li>Milan</li>
<li>Pise</li>
</settlement>
</list>
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<name sortKey="Battaglia, Cristina" sort="Battaglia, Cristina" uniqKey="Battaglia C" first="Cristina" last="Battaglia">Cristina Battaglia</name>
<name sortKey="Battaglia, Cristina" sort="Battaglia, Cristina" uniqKey="Battaglia C" first="Cristina" last="Battaglia">Cristina Battaglia</name>
<name sortKey="Bellis, Gianluca De" sort="Bellis, Gianluca De" uniqKey="Bellis G" first="Gianluca De" last="Bellis">Gianluca De Bellis</name>
<name sortKey="Benelli, Matteo" sort="Benelli, Matteo" uniqKey="Benelli M" first="Matteo" last="Benelli">Matteo Benelli</name>
<name sortKey="Bonora, Elena" sort="Bonora, Elena" uniqKey="Bonora E" first="Elena" last="Bonora">Elena Bonora</name>
<name sortKey="Cifola, Ingrid" sort="Cifola, Ingrid" uniqKey="Cifola I" first="Ingrid" last="Cifola">Ingrid Cifola</name>
<name sortKey="D Urizio, Romina" sort="D Urizio, Romina" uniqKey="D Urizio R" first="Romina" last="D Urizio">Romina D Urizio</name>
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<name sortKey="Giusti, Betti" sort="Giusti, Betti" uniqKey="Giusti B" first="Betti" last="Giusti">Betti Giusti</name>
<name sortKey="Magini, Pamela" sort="Magini, Pamela" uniqKey="Magini P" first="Pamela" last="Magini">Pamela Magini</name>
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<name sortKey="Pippucci, Tommaso" sort="Pippucci, Tommaso" uniqKey="Pippucci T" first="Tommaso" last="Pippucci">Tommaso Pippucci</name>
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<name sortKey="Tattini, Lorenzo" sort="Tattini, Lorenzo" uniqKey="Tattini L" first="Lorenzo" last="Tattini">Lorenzo Tattini</name>
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</record>
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