Convert SNP IDs as chr:pos:effect allele:ref allele to rsIDs
I have a set of 58000 SNPs for which the SNP ID is in the format of:
chr:pos:effect allele:ref allele (Grch37 build), but I need to convert this to rsID where one is available for the SNP. I’ve tried using Variant Recoder command line tool from biomart, however I couldn’t get it to work and am keen to find alternative solutions.
This SNP ID conversion is so I can use them as input to 2 sample MR, however the majority of these 58000 SNPs will not be independent, so an alternative if it’s possible is to clump the SNPs based on the ID format I have (chr:pos……), and I could then use the reduced, clumped, list of SNPs as input to the web based version of Variant Recoder which is working for me but takes maximum 1000 SNPs, but as far as I can tell rsIDs are needed for clumping.
I would be very grateful for advice!
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