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Filter out potential markers using SNAP tools.
Hi,
I'm running a simple project: find potential SNP-s associated with a specific disease among known genes (done, few SNP-s per gene), increase a "resolution" of my study, choose all known SNP-s within a genes and look for more specific markers (to be done).
Assuming that I already know all SNP-s within gene markers, now I need to reduce the total cost of the study and exclude from the analysis (genotypic) SNP-s with high LD.
Is this approach OK? What do you think? If yes, can I use SNAP tool for that (CEU, 1000 Project), and keep only those RSs with e.g. R^2 below 0.8 and skip RSs in high LD? Are there any tools I can use to speed up this primary step, or should I look at every pair of markers and keep those in low LD?
Thank you in advance, Witold.
I'm running a simple project: find potential SNP-s associated with a specific disease among known genes (done, few SNP-s per gene), increase a "resolution" of my study, choose all known SNP-s within a genes and look for more specific markers (to be done).
Assuming that I already know all SNP-s within gene markers, now I need to reduce the total cost of the study and exclude from the analysis (genotypic) SNP-s with high LD.
Is this approach OK? What do you think? If yes, can I use SNAP tool for that (CEU, 1000 Project), and keep only those RSs with e.g. R^2 below 0.8 and skip RSs in high LD? Are there any tools I can use to speed up this primary step, or should I look at every pair of markers and keep those in low LD?
Thank you in advance, Witold.