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EXCAVATOR2
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EXCAVATOR2

EXCAVATOR2 is a tool for detecting copy number variation (CNV) in whole-genome exome sequencing data. The EXCAVATOR2 algorithm uses a hidden Markov model (HMM) and a method that classifies genomic regions into five CNV states. EXCAVATOR2 is an enchanced version of EXCAVATOR (see links).



EXCAVATOR2

EXCAVATOR2 is a tool for detecting copy number variation (CNV) in whole-genome exome sequencing data. The EXCAVATOR2 algorithm uses a hidden Markov model (HMM) and a method that classifies genomic regions into five CNV states. EXCAVATOR2 is an enchanced version of EXCAVATOR (see links).

Topic

Genetic variation

Details

  • Operation: Variant calling
  • Software interface: Command-line user interface
  • Language: bash;Fortran,R
  • Operating system: Mac OS X, Linux
  • License: Not stated
    • Cost: Free
  • Version name: 1.1.2
    • Maturity: Beta
  • Credit: Flagship project InterOmics, Italian Ministry for Instruction University and Research (MIUR) and CNR organisations; Italian Ministry of Health, Young Investigators Award for the Project GR-2011-02352026 ‘Detecting copy number variants from whole-exome sequencing data applied to acute myeloid leukemias’.
  • Contact: Romina D'Aurizio romina.daurizio _at_ gmail.com | Alberto Magi albertomagi _at_ gmail.com
  • Collection: -

Publications

D'Aurizio R, Pippucci T, Tattini L, Giusti B, Pellegrini M, Magi A "Enhanced copy number variants detection from whole-exome sequencing data using EXCAVATOR2." Nucleic Acids Res. 2016 Nov 16;44(20):e154. Epub 2016 Aug 9. https://doi.org/10.1093/nar/gkw695
PMID: 27507884
PMCID: PMC5175347


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