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Meta-analysis of genomewide association scans
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Convert coordinates of GRCh38 to 37, but the SNPids keep the same, can I meta it via Metal with other GWAS Summary data ? #38

Open dqq0404 opened 4 months ago

dqq0404 commented 4 months ago

I used liftover to convert GRCh38 to GRCh37, but the SNP id keep the same. Do I have to continue using the transformed coordinates to match to the SNP id of the GRCh37? I randomly searched the SNP ids corresponding to several converted coordinates on NCBI and found that the snp ids did not change, so I am not sure whether the two versions only changed the location information while the SNP ids did not change.

Lloyd-LiuSiyi commented 2 days ago

When the reference genome updates from hg19 to hg38, all given rsIDs for SNPs remain unchanged. The update only "updates" the coordinates of existing SNPs, adds information to newly discovered SNPs and assigns them new rsIDs.