Question: Setting a threshold based on effective number of independent Snps in GWAS.
gravatar for Abbas.M
4 weeks ago by
Abbas.M0 wrote:

I want to set a threshold of GWAS based on effect number of independent snps in my genotype data. As i read in literature, most of the recently published papers have set threshold by this way. At first they calculated effective number of independent snps in their snp data. Then applied a basic bonferroni correction. Lets suppose, if effective number of independent markers are 20000 then the threshold would be like this, 0.05/20000, here 0.05 is the 5% error rate. Genetic type 1 error calculator can do it, but their website is unstable and i am unable to access it. Is there any alternative methods to estimate independent number of markers in a SNP data? Here is the link of the paper, in which they proposed this method, and other studies using their proposed method.,parameters%3A%20-maxdistance%202000%20-minMAF%200.05%20-hwcutoff%200%20%2829%29.

genome snp R gene • 127 views
ADD COMMENTlink modified 4 weeks ago by Nicolas Rosewick9.3k • written 4 weeks ago by Abbas.M0
gravatar for Nicolas Rosewick
4 weeks ago by
Belgium, Brussels
Nicolas Rosewick9.3k wrote:

You could prune your dataset with plink : and then count how many SNP are in the resulting file.

In Anderson et al. 2010 good GWAS practices paper, to compute a pruned dataset :

plink --file raw-GWA-data --exclude high-LD-regions.txt --range --indep-pairwise 0.15 50 5 0.2 --out raw-GWA-data
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Nicolas Rosewick9.3k

thank you so much for answering my question. I did LD pruning in plink, but i was not sure about it, whether we can set a threshold of gwas on the basis of LD pruned snps. Once again thanks

ADD REPLYlink written 4 weeks ago by Abbas.M0
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