WGAViewer

Frequently asked questions

1. For installation/connection related questions, see here. This page also discusses the installation-related issues.

2. Q: The annotation procedures work for the example data sets, but not for mine.

A: A common reason we found is that the SNP designation label in some map file, typically rs numbers, was capitalized. WGAViewer is case-sensitive and will search for exact match to gene and SNP entries in online databases. Therefore, an rs number of "rs12345" will work, while "RS12345" will not.

If this is not your case, file a problem report to the developer.

3. Q: How do I perform genome-wide association test using WGAVIewer?

A: WGAViewer is a tool for annotating and helping interpret statistical results generated from a genome-wide association study (GWAS). The result from a GWAS is the input for WGAViewer. You cannot perform genome-wide association test using WGAViewer. You will have to use other software to generate statistical signals first, for example, PLINK.

4. Q: Are you still working on and will keep updating this software?

A: Yes. Absolutely.

5. Q: Does WGAViewer support smaller-scale genetic studies. i.e., studies with a smaller number of genetic polymorphisms than a GWAS?

A: Yes. You can make the input for WGAViewer as usual. You may want to load an additional anchor set with your data to increase the annotation density of your project, though. This function is through menu "Database -> Additional markers".

6. Q: Will WGAVIewer expand to species other than human, for example, canine?

A: Although this is a very interesting topic, currently we do not have such expansion plan.

7. Q: problem: We use WGAViewer under LINUX and try to open any HTML tags; But nothings happens. Only with truss/strace we found out, that external program 'htmlview' was searched - and not found.

A: solution: we linked our 'firefox' in $HOME/bin/ to htmlview - and now it works :-) See also here.

 

For other questions, please send an email to: Dongliang Ge, PhD, Duke Institute for Genome Sciences & Policy, Center for Human Genome Variation.