Get variant info from UK Biobank imputed genotype MFI files — get_imputed_variant

For a given set of genomic coordinates (position in build 37) get the UK Biobank imputed genotype variant IDs from the MFI files.

Usage

get_imputed_variant_info(varlist, verbose = FALSE)

Arguments

varlist: A data frame. Contains at least two columns: `chr` and `pos` (b37). Other columns are ignored.
verbose: Logical. Be verbose (show individual steps), default=FALSE

Value

A data frame of variants with added "ukb_rsid" column (also returns alleles, MAF and INFO)

Author

Luke Pilling

Examples


# Example where RSID is only known for some variants
varlist1 <- data.frame(rsid=c("","rs564086017",""), chr=c(1,2,22), pos=c(10616, 10180, 16050435))
varlist2 <- get_imputed_variant_info(varlist1)