function to use ensembl API to convert rsid to hg38 coordinates ... note the seqnames

gistfile1.txt

get_rslocs_38 = function(rsids = c("rs6060535", "rs56116432")) {
 server <- "https://rest.ensembl.org"
 ext <- "/variant_recoder/homo_sapiens"
 r <- httr::POST(paste(server, ext, sep = ""), 
       httr::content_type("application/json"), 
       httr::accept("application/json"), 
       body = list(ids=rsids), encode="json")
 httr::stop_for_status(r)
 ans = rjson::fromJSON( rjson::toJSON( httr::content(r)))
 ids = lapply(ans, "[[", "id")
 spd = sapply(lapply(ans, "[[", "spdi"), "[", 1)
 sspd = strsplit(spd, ":")
 chrs = sapply(sspd, "[", 1)
 locs = as.numeric(sapply(sspd, "[", 2))+1
 ans = GenomicRanges::GRanges(chrs, IRanges::IRanges(locs, width=1))
 GenomeInfoDb::genome(ans) = "GRCh38"
 names(ans) = ids 
 ans 
}

> get_rslocs_38()
GRanges object with 2 ranges and 0 metadata columns:
                 seqnames    ranges strand
                    <Rle> <IRanges>  <Rle>
   rs6060535 NC_000020.11  35647600      *
  rs56116432 NC_000009.12 133256042      *
  -------
  seqinfo: 2 sequences from GRCh38 genome; no seqlengths