I am interested in annotating a list of variants using VARAdb. My coordinates use the GRCh38 (hg19) reference genome. However, I do not know which coordinate system VARAdb uses.
A section of the VARAdb publication reads: "GWAS have provided a large amount of data associating genetic variants with common phenotypes. We collected risk SNPs fromfive sources, including theNHGRI GWAS Catalog (29), GWASdb v2.0 (30), GAD (31), Johnson and O’Donnell (32), and GRASP v2.0 (33). Then, we filtered risk SNPs ofwhich ‘Variant ID’which are not ‘rsID’ and transformed locations of risk SNPs from the GRCh38 assembly version into the hg19 version in the GWAS Catalog. Finally, we obtained 1 515 001 risk SNPs associated with diseases, traits and phenotypes."
which makes me think that they may be using the hg19 genome, but I am not sure.
So, my question is:
Which human reference genome version does VARAdb use?
VARAdb database: http://www.licpathway.net/VARAdb/search.php
VARAdb publication: https://pubmed.ncbi.nlm.nih.gov/33095866/