Dear Bioconductors,

I have a long list of dbSNP identifiers (e.g. rs7335199), some of which are outdated and now represented by a new identifier.

For example, the following call to ensembl's REST API reveals that variant rs7335199 is now referred to as rs3.

curl 'https://rest.ensembl.org/variant_recoder/human/rs7335199?fields=id' -H 'Content-type:application/json'

[{"input":"rs7335199","id":["rs3"]}]

My goal is to retrieve the genome coordinates (GRCh38) and, if available, the current variant identifier for millions of variants. So far, I have tried

1. ensembl's REST service: great for smaller queries, but not for millions of variants
2. the biomaRt Bioconductor package: works great, but takes a long time to query
3. the SNPlocs.Hsapiens.dbSNP150.GRCh38 Bioconductor package: contains the coordinates for up-to-date variants (e.g. rs3) but not outdated ones (e.g. rs7335199). 

library(SNPlocs.Hsapiens.dbSNP150.GRCh38)
snps <- SNPlocs.Hsapiens.dbSNP150.GRCh38

snpsById(snps, c("rs3", "rs7335199"), ifnotfound = "drop")
GPos object with 1 position and 2 metadata columns:
      seqnames       pos strand |   RefSNP_id alleles_as_ambig
         <Rle> <integer>  <Rle> | <character>      <character>
  [1]       13  31872705      * |         rs3                Y
  -------
  seqinfo: 25 sequences (1 circular) from GRCh38.p7 genome

What is the recommended way to obtain

• the current dbSNP identifier and
• their genomic coordinates for a mixed list of current and deprecated variant ids?

Any pointers would be great!

Many thanks,

Thomas