Question: Find region that full captures association signal
gravatar for User 7754
20 months ago by
User 7754240
United Kingdom
User 7754240 wrote:


Are there any softwares or scripts to define a genomic region around an association signal in GWAS? I know people define usually a set amount (e.g. 200kb) around the most associated SNP, or first find the index SNPs in Plink and then limit these by LD and pvalue, but I was wondering if there is even a simpler way (just based on pvalue) to go right and left of the most associated SNP, and stop where there is no more associated SNPs at a pvalue < 0.5 for example. It seems like something like this would be very useful in the world of GWAS, there must be scripts/packages/softwares that do that?

Thank you for any suggestions!

pvalue ld gwas • 410 views
ADD COMMENTlink modified 20 months ago by christopher medway450 • written 20 months ago by User 7754240
gravatar for christopher medway
20 months ago by
Cardiff, UK
christopher medway450 wrote:

I think you are looking for a method that falls within the suite of "Finemapping Tools". Here is a nice review. I know there are tools that seek to identify a set of 'Credible' SNPs - the genomic coordinates that these span may help you to define a genomic region.

ADD COMMENTlink written 20 months ago by christopher medway450
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