liftover using GWAS summary data and PLINK binary files (bed/bim/fam)

Question

[Joey]

Hi,

I have a GWAS summary data (chr, snp, bp beta, se etc.) file based on the 1000G Aug 2010 1000G imputation (GRCh37.p13).

The genetic data for calculating LD was given to me in PLINK binary/best guess genotype format (bed/bim/fam) and was based on a newer imputation (1000G March 2012; GRCh38).

I want to convert the SNPs and positions in the summary data file to the same build as the PLINK data i.e. update the positions, rename/drop SNPs if applicable.

Is there a software or tools to do this?

Thanks,

-Joey

[Junhao]

If I understand it correctly, liftover only convert the bed file, not the GWAS summary stats, right?

Answer 1

[dora]

You can look at the liftOver tool here. It's very comprehensive for your purpose.