Tool to annotate variants with RSIDs

This script and accompanying dbsnp file can be used to add RSID annotation to a file containing chromosome, position, reference allele, and alternate allele.

Usage instructions in GitHub repository

[https://github.com/FINNGEN/commons/blob/master/annotate_rsids/README.md]

Location of the script and readme in the Sandbox

/finngen/library-green/scripts/annotate_rsids/

Example use of the script (show help page):

python3 /finngen/library-green/scripts/annotate_rsids/rsidify.py -h

Dbsnp REFERENCE files

We provide two dbsnp REFERENCE files for annotation. These files can be used for files on human genome build 38 only (e.g. all FinnGen association analyses are compatible).

The main annotation file contains all variants in DBNSP (/finngen/library-green/dbsnp/dbsnp-b155-hg38-left-align-split.vcf.gz).

For convenience, we also provide another file (/finngen/library-green/dbsnp/dbsnp-b155-GRC38.13.left_align_split.finngen_panel_4.1_variants.small.gz), containing only variants that are on sisu4.1 imputation panel.

The results will be identical but using only subset of variants will run much faster. If you are unsure which variants you have, use the full file.\