Question: Tagsnps: Is There An Easy Way To Select Tagsnps From The 1000 Genomes Project?
3
gravatar for Arielsonique
9.2 years ago by
Arielsonique30
Arielsonique30 wrote:

Hi, I would like to use the latest 1000 genomes project to pick tag SNPs for a genetic association study. Is there an efficient and quick way to do this? Are there any tutorials or software that make the task of picking tagSNPs from the 1000 genomes project easier? Thanks for your time!

genome genetics selection snp • 6.3k views
ADD COMMENTlink modified 9.2 years ago by Larry_Parnell16k • written 9.2 years ago by Arielsonique30
3
gravatar for Thomas
9.2 years ago by
Thomas730
Copenhagen, DK
Thomas730 wrote:

To get proxy SNPs, r^2, Dprime etc. You can have a look at the following link from BROAD (1000G is included):

http://www.broadinstitute.org/mpg/snap/ldsearchpw.php

all the best Thomas

ADD COMMENTlink written 9.2 years ago by Thomas730

SNAP is out tool of choice - and we do a lot of tag SNP work - because it contains the phase I 1000G data. For absolute LD, use r^=1.0; for strong LD, use r^2=0.8.

ADD REPLYlink written 9.2 years ago by Larry_Parnell16k

Larry, is there any criteria on physical position, genetic position in ASSAY selection on chromosome, i am working on selecting assay in rice and i have more than 80 SNP assays with their physical and genetic position on chromosome and now i want to reduce this to 10 SNPs per chromosome. i request you to share your knowledge or any other articles useful for me in this work. I am sorry if posted this in wrong.

ADD REPLYlink written 6.9 years ago by blacktomato2760

Thanks very much! I will play around with SNAP. As I understand it, SNAP gives you all the SNPs that are say, in r^2=0.8 with another SNP on a given gene. How do you decide which of the 0.8 LD SNPs to then pick?

ADD REPLYlink written 9.2 years ago by Arielsonique30

That is a good question. For some reason 0.8 is a global accepted threshold for r2 when you tag a specific gene/region. I should add that I work within genetic association of common diseases. It might be different for other diseases.

ADD REPLYlink written 9.2 years ago by Thomas730

I wish there were something like Snagger to load the 1000genomes data and pick SNPs. I am not very confident about which SNPs to eliminate in any given LD block all correlated at 0.8. How would you guys do it?

ADD REPLYlink written 9.2 years ago by Arielsonique30
2
gravatar for Larry_Parnell
9.2 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

ArielSonique asked: How do you decide which of the 0.8 LD SNPs to then pick?

I usually don't because it can be a lot of computational work to decide the putative function of each SNP and to then prioritize all those proxy SNPs to the one (maybe two) that you'll genotype. Search for this topic on BioStar as it has been asked before and many great answers were provided. Try this question, for example.

That said, I'd let the genotyping data I have - say from GWAS - tell me which SNPs already have genotyping data. Or, we would use data from the genotyping assay provider tell us which SNP(s) to genotype because they had the assay for sale (as opposed to designing a new assay for another SNP).

ADD COMMENTlink modified 10 months ago by RamRS28k • written 9.2 years ago by Larry_Parnell16k
1
gravatar for Brianc
8.7 years ago by
Brianc70
Brianc70 wrote:

Tagger by the Broad Institute.

http://www.broadinstitute.org/mpg/tagger/server.html

Web-based interface, sends you a link via email once it's done.

ADD COMMENTlink written 8.7 years ago by Brianc70
0
gravatar for romsen
7.7 years ago by
romsen60
romsen60 wrote:

Is there a tool that generate tagSNPs for common biallelic CNVs?

ADD COMMENTlink written 7.7 years ago by romsen60
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