Hello everyone,
I have a .txt with columns - CHR , SNPID , Position, P value , TA, OA , Frequency , Beta, SE and N.
My goal is to perform LD clumping. I tried LDLinkR package which has not been an efficient method since I had nearly 41,000 SNPs. Please advise how I may convert the .txt file into .ped and .map files to use PLINK for LD clumping.
Thank you for your help.
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written
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jyothisrilok •
Hello jyothisrilok,
PLINK format files consist of individual Genotype data.
Since they cannot be converted from summary data, please consider other methods aside from converting to PLINK format.
Consider the following alternative methods:
Perform approximate LD pruning using a reference panel dataset, such as the 1000 Genomes Project. However, caution is needed in the choice of data populations.
Obtain actual sample genotype data.
Thank you so much Hirofumi. I am quite new to GWAS studies and this helped me understand how different are summary stats from the genotype data. I used LD_clumping in R and it worked. Thank you.
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