WebJan 16, 2024 · The --clump command is designed to help with this. --clump loads the named PLINK-format association report (s) (text files with a header line, a column containing variant IDs, and another column containing p-values) and groups results into LD-based clumps, writing a new report to plink .clumped. Gzipped reports are permitted. WebClumping window, default is 10000. clump_r2. Clumping r2 cutoff. Note that this default value has recently changed from 0.01 to 0.001. clump_p1. Clumping sig level for index …
TwoSampleMR/ld.R at master · MRCIEU/TwoSampleMR · …
WebClumping. Here, we use an LD reference panel to identify SNPs that are in LD with the top signals from a GWAS. The algorithm sequentially chooses the top SNP, removes all SNPs in LD above some threshold within some window, then goes on to the next top hit and repeats the pruning process, until no more SNPs are left above the specified p-value … WebTechnical note: SNPsnap writes a temporary .assoc file (two column file with the field headers "SNP" and "P") for the input SNPs. The values in the "P" column is set to a fixed … fanfic crying a river of tears
PLINK - Harvard University
WebOct 11, 2016 · Run PLINK clump command using default settings, but might want to change with different nominal significance thresholds. plink -vcf results/1KGgeno.vcf --clump data/eSNP.assoc. PLINK clump command identifies 8 independent eSNPs in the region. Next step, extract independent eSNPs from individual level genotype data, build MR risk … WebNov 8, 2024 · Uses PLINK clumping method ('–clump' command), where a greedy search algorithm is implemented to randomly select a variant (or the variant with the lowest p-value, if a user wish to), referred to as the index SNP, and remove all variants within a certain kb distance in linkage disequilibrium with the index SNP, based on an r-squared threshold … WebJul 24, 2024 · UK Biobank data on height (\(h_{SNP}^2\) = 0.49 8), FVC (\(h_{SNP}^2\) = 0.23 8) and hand grip (\(h_{SNP}^2\) = 0.11 8) were randomly split into two sets of 100,000 individuals and used as base ... cork o\u0027connor series goodreads