Populate missing RSIDs

[apriha]

Utilize NCBI's Variation Services API to populate missing RSIDs.

An idea for how this could be performed... For all SNPs in a dataset, lookup RSIDs in batches of 50k SNPs (1 request / second) using the VCF endpoint. Then, use the resulting information to populate any missing RSIDs. However, note that this method would require the REF allele and a valid ALT allele.

As an example, one row for this query (using GRCh38) could be constructed as follows:

1 817186 . G A,C,G,T

Query:

curl -X POST "https://api.ncbi.nlm.nih.gov/variation/v0/vcf/file/set_rsids?assembly=GCF_000001405.38" -H "accept: text/plain; charset=utf-8" -H "Content-Type: text/plain; charset=utf-8" -d "1\t817186\t.\tG\tA,C,G,T"

Which would return:

1 817186 rs3094315 G A,C,G,T

This could also be used to verify SNP positions and help with #6.

Thanks to @gedankenstuecke for helping develop the idea!