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Using XCAVATOR and EXCAVATOR2 to Identify CNVs from WGS, WES, and TS Data.

Authors
  • D'Aurizio, Romina1
  • Semeraro, Roberto2
  • Magi, Alberto2
  • 1 Institute of Informatics and Telematics, National Research Council, Pisa, Italy. , (Italy)
  • 2 Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy. , (Italy)
Type
Published Article
Journal
Current protocols in human genetics
Publication Date
Jul 05, 2018
Identifiers
DOI: 10.1002/cphg.65
PMID: 29975818
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Copy Number Variants (CNVs) are structural rearrangements contributing to phenotypic variation but also associated with many disease states. In recent years, the identification of CNVs from high-throughput sequencing experiments has become a common practice for both research and clinical purposes. Several computational methods have been developed so far. In this unit, we describe and give instructions on how to run two read count-based tools, XCAVATOR and EXCAVATOR2, which are tailored for the detection of both germline and somatic CNVs from different sequencing experiments (whole-genome, whole-exome, and targeted) in various disease contexts and population genetic studies. © 2018 by John Wiley & Sons, Inc. © 2018 John Wiley & Sons, Inc.

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