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Frequently Asked Questions

 

Q: Can I use CONAN to detect CNVs?

No, CONAN was developed for the conduction of GWAS based on CNVs. In order to use CONAN, CNVs must be determined by using third-party tools like PennCNV, QuantiSNP, Birdsuite or Cokgen.

 

Q: What are the advantages of using an Oracle Database Server?

If your study is very small (a few hunderds subjects) you don't need the oracle database and the performance of the local database is sufficient. But if your study consists of several thousand subjects you can improve the performance drastically by usig an Oracle database server. Moreover, you can share your results with other members of your lab by using the same database server in your local network,

 

Q: Which algorithms are you using?

Please read the method section in our paper.

 

Q: Which file format does CONAN support?

CONAN supports the following file formats for CNV data:

  • PennCNV
  • QuantiSNP
  • Affymetrix Genotyping Console
  • CSV Files (see the user manual for an example)
  • Excel Files (see the user manual for an example)

CONAN supports the following file formats for phenotypes:

  • CSV Files (see the user manual for an example)
  • Excel Files (see the user manual for an example)

CONAN supports the following chip arrays:

  • Affymetrix 500k
  • Affymetrix 5.0
  • Affymetrix 6.0

 

Q: How many samples can CONAN handle?

CONAN was successfully tested with a population study consisting of 1,800 subjects.

 

Q: Which paper should I cite for CONAN?

Our paper about CONAN was published in BMC Bioinformatics. In case you like the software, we would appreciate if you cite the software and the related publication:

Forer et al., CONAN: copy number variation analysis software for genome-wide association studies BMC Bioinformatics 2010, 11:318

 
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