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EXCAVATOR
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EXCAVATOR

EXCAVATOR is a tool for detecting copy number variation (CNV) in whole-genome exome sequencing data. The EXCAVATOR algorithm uses a hidden Markov model (HMM) and a method that classifies genomic regions into five CNV states.



EXCAVATOR

EXCAVATOR is a tool for detecting copy number variation (CNV) in whole-genome exome sequencing data. The EXCAVATOR algorithm uses a hidden Markov model (HMM) and a method that classifies genomic regions into five CNV states.

Topic

Genetic variation

Details

  • Operation: Variant calling
  • Software interface: Command-line user interface
  • Language: Perl
  • Operating system: Mac OS X, Linux
  • License: Not stated
    • Cost: Free
  • Version name: 1 (v 2.2 is availbe. See links)
    • Maturity: Beta
  • Credit: The Cariplo Foundation, Estonian Ministry of Education and Research, European Commission FP7 funding, Project CHERISH, the Italian Ministry of Health’s Young Investigators Award.
  • Contact: Alberto Magi:albertomagi _at_ gmail.com;Lorenzo Tattini:lorenzotattini _at_ gmail.com;IngridCifola:ingrid.cifola _at_ itb.cnr.it;Romina D’Aurizio:romina.daurizio _at_ gmail.com;Matteo Benelli:matteo.benelli _at_ gmail.com;EleonoraMangano:eleonora.mangano _at_ itb.cnr.it;CristinaBattaglia:cristina.battaglia _at_ unimi.it;Elena Bonora:elena.bonora6 _at_ unibo.it;Ants Kurg:akurg _at_ ebc.ee;Marco Seri:marco.seri _at_ unibo.it
  • Collection: -

Publications

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 "EXCAVATOR: detecting copy number variants from whole-exome sequencing data." Genome Biol. 2013;14(10):R120. https://doi.org/10.1186/gb-2013-14-10-r120
PMID: 24172663
PMCID: PMC4053953


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