Hi everyone,
It has been recommended that in order to well design your genetic association study, it is better to choose tagSNPs. I've started the process using UCSC and HapMap databases to get a sample genotypes for the gene of interest. Then, using Haploview program, I obtained a list of TagSNPs under the results button of the Tagger option. Unfortunately, the list obtained was different from that in the Haplotypes option---Show tags in blocks( in the same program ). It was also different from that showed in the HapMap database--tag SNP Picker. Therefore, I was confused about which list is the correct one to be chosen to complete the process with ( testing the functionality and previously published clinical associations ).
So, kindly I'm looking for your help to solve this problem.
Thanks a lot.
Why do you need tagSNPs, are you designing a new Chip? Nowadays it may be cheaper to buy a commercial chip from Illumina/Affimetrix, or do NGS directly.