Compute ld and genomic distance using clump function in plink
Hi All,
This is a plink question. I need to compute the genomic distance and LD between the variants and its corresponding index (let's say variants within 1-Mb[?] "clumps"). I have a list of index variants index_variants.txt and I tried the following command but it generates error (Error: Invalid --clump-p1 parameter). Can someone please guide me how to perform this?
plink --bfile bfile --clump assoc_results_withBETA --clump-p1 index_variants.txt --clump-kb 1000 --r2 --out clump_output
index_variant.txt
chr12:6883381:C:T
chr13:6296822:GC:G
chr14:1120198:A:G
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The
--clump-p1should define significance threshold for the index SNPs and not the list of SNPs for e.g.,--clump-p1 0.0001. Please check out this page.