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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.


Genetic variation


  • 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_;Lorenzo Tattini:lorenzotattini _at_;IngridCifola:ingrid.cifola _at_;Romina D’Aurizio:romina.daurizio _at_;Matteo Benelli:matteo.benelli _at_;EleonoraMangano:eleonora.mangano _at_;CristinaBattaglia:cristina.battaglia _at_;Elena Bonora:elena.bonora6 _at_;Ants Kurg:akurg _at_;Marco Seri:marco.seri _at_
  • Collection: -


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.
PMID: 24172663
PMCID: PMC4053953

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