Looking up chromosome and position for large sets of rs IDs

Often GWAS datasets are shared with only the rs ID. To upload to the OpenGWAS database we need chromsome, position, effect allele, non-effect allele - rs ID is not used primarily.

The get_positions() function provides a convenient way to just lookup the chromosome and position from rs ID, though be warned it is quite slow, e.g. might take up to 30 minutes for 10 million SNPs.

library(GwasDataImport)
library(data.table)

# Read in a small dataset
fn <- system.file("extdata/pos_0002.txt.gz", package="GwasDataImport")
a <- fread(fn)

# list of rsids
rsid <- a$RSID

# get positions
pos <- get_positions(rsid)