Dear Biostar Community,
Being rather new to the field of bioinformatics I would like to ask for your help identifying tag SNPs for ONE certain gene.
Does it theoretically suffice to generate a LD Plot and select a tagSNP simply by reading it?
For example in this picture rs727153 covers most other SNPs in this region. Whats the difference to using programs that identify tagSNPs (like Tagger)?
How can I obtain a list of SNPs for my analysis, with or without annotations?
So far I have found several methods, but the numbers of SNPs for the same gene vary, therefore I don't know which list is the right one
- GeneCard -> table of around 300 SNPs
- Hapmap.org -> dump SNP genotype data -> 20 SNPs
- Pubmed->SNP search-> dbSNP batch report in Display settings -> 600 SNPs (including some which have merged into others, but I could not filter them)
- SySNP -> 155 SNPs
Do you think, that I will reach my goal using Haploview? My problem is, that I only managed to analyze the hapmap data dump (20 SNPs) so far. Unfortunately the information about the input files for this program or other questions here on Biostar do not explicitly explain how to create or obtain the right formats out of simple SNP list .txt files for different programs, including Haploview.
Thank you very much!
Here is another tool Snagger, which lets you prioritise certain "favourite" SNPs