Question: liftover using GWAS summary data and PLINK binary files (bed/bim/fam)
1
gravatar for Joey
4.3 years ago by
Joey410
Seattle
Joey410 wrote:

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

plink liftover snp gwas • 3.2k views
ADD COMMENTlink modified 3.8 years ago by dora 90 • written 4.3 years ago by Joey410
2
gravatar for dora
3.8 years ago by
dora 90
European Union
dora 90 wrote:

you can look at the liftOver tool here http://genome.sph.umich.edu/wiki/LiftOver. It's very comprehensive for your purpose. 

ADD COMMENTlink written 3.8 years ago by dora 90
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