Tutorial 6: Remap genomic coordinates to a different genome assembly

library(gwasglue2)
library(ieugwasr)
devtools::load_all("../") # this was added just for development

gwasglue2 has a liftover() function to remap genomic coordinates from different genome assemblies to the same reference build.

gwasglue2 uses the chain files and human genome nomenclature of ENSEMBL (“NCBI34”, “NCBI35”, “NCBI36”, “GRCh37” and “GRCh38”).

In this, tutorial we have GWAS summary data obtained from IEU OpenGWAS through the ieugwasr package. The data was built under the “GRCh37” genome assembly and we want to remap it to “GRCh378”.

First, we create a SummarySet object that we name sumset1 providing in the build argument the genome assembly used to build the GWAS summary data. We can check it in the metadata.

data1 <- ieugwasr::associations(variants = "5:74132993-75132993", id = "ukb-d-I9_IHD")

sumset1 <- create_summaryset(data1, build ="GRCh37")
getMetadata(sumset1)

Then we perform the liftover. We can first download the chain file followed by the liftover(). In this case we need to give the genome assemblies to “lift from” and to “lift to” :

sumset1_lift <- download_chainfile(from = "GRCh37", to = "GRCh38") %>%
                liftover(sumset1, chainfile = ., to = "GRCh38")

Or simply provide directly to liftover() the genome assembly to “lift to”. In this case, the function will check the build to “lift from” in the metadata of sumset1 and download the chain file.

sumset1_lift <- liftover(sumset1, to = "GRCh38")