How To Use The Scan Annotation Software

Question

[giacomogiacalone]

Hi everybody!

I am using SCAN annotation tool to annotate a list of SNPs from my GWAS. In particular I am trying to use "LD annotations" option to look at genes in LD with my variants. However I didn't understand on which population is the LD calculation made on: indeed it is not specified (in the paper they don't say it clearly, for other options they use CEU and YRI). Have anybody here ever used SCAN tool? What do you think about it?

Thank you!

Bye

Giacomo

[Zev.Kronenberg]

If you have NGS data maybe you should think about trying the VAAST pipeline. It is an annotation tool and probabilistic gene hunter. http://www.yandell-lab.org/software/vaast.html