Get Rs Number Based On Position (6 million SNPs)

Get Rs Number Based On Position (6 million SNPs)


I know this question has sort of been asked before….but I need to know which method would be the most efficient way to get the Rs numbers based on position (hg19)

I’ve considered looping through two files, the .txt file (with the positions) and a .vcf file with all known variants from Kaviar Genomic Variant Database, locally…but that would take forever…

would installing a partial UCSC genome MySQL database locally be a better idea? 

Any suggestion would be great…be as detailed as possible pls :).

PS: This .txt file is an output from METAL, and unfortunately I need all 6.4M SNPs for my project at this point



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written 5.9 years ago by



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