I have a list of about 250 SNPs. I want to obtain the proxy SNPs for them using the 1000 genomes. I have downloaded corresponding .vcf and .ped files from 1000 genomes. I have also used PLINK to obtain the .bim, .fam and .bed files.
How do I proceed to determine the proxy SNPs without using any software?
Thank you.
Get LD for selected SNPs using plink --r2. Then pick any proxy SNP having highest LD score.
Why not using other software? We could, for example, use PriorityPruner which is specifically designed to pick proxies with prioritisation, i.e. when SNP1 is in LD with SNP2 and SNP3, it will prioritise based on other features of the SNP (like pvalue, frequency, annotations, etc.).
PriorityPruner is a software program which can prune a list of SNPs that are in high linkage disequilibrium (LD) with other SNPs in the list, while preferentially keeping SNPs of higher priority (e.g., the most significant SNPs in a genome-wide association study). The process of pruning SNPs based on LD is sometimes referred to as "LD clumping".
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Thank you very much. I am using snpStat to calculate the LDs.