Hello there,
I am looking at the ROSMAP SNP data (syn3221153). I checked a few SNPs. It seems that their coordinates are based on neither GRCh37 or CRCh38.
Taking rs12563338 as an example, its coordinate is 1188481 on chr1 in ROSMAP data, but the positions in GRCh37 and CRCh38 are 1198618 and 1263238, respectively. As another example, the position of rs11240777 in ROSMAP, GRCh37 and CRCh38 are 788822, 798959 and 863579, respectively.
I would like to use coordinates in my QTL analysis, but am now not sure which genome coordinate version should be used. Will you please so kind as to help me understand the SNP coordinates in ROSMAP? Your help would be highly appreciated!
Looking forward to you reply. Thanks!
Best,
Hongdong
Created by Hongdong Li hongdong Hi,
I was wondering if it is solved in your research? If I use GRCh37 or CRCh38 as the coordinates, which one should be selected?
Your sincere help would be highly appreciated!
Best,
Qinglong Hi @jgockley , that's very helpful. Thanks, ;-)
Hi @hongdong
The majority of the genotyping data was produced in 2009 so those files will actually be in hg18 coordinates. Take a look at the imputed files, they might be in hg19. Plink should have a flag to convert dosage formats, I'd start with chr21 or 22 as they are smaller.
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Genome coordinate version of SNPs in ROSMAP? page is loading…