Validate liftover results against dbSNP #53
Description
Feature description
dbSNP's notion of a "variant" is a little crazy (it's like an inconsistently-shaped category) but it does tend to include genomic expressions for both build 37 and 38. It'd be nice to perform a dbSNP-wide validation experiment to see how much their liftover mappings align with those of this tool.
Use case
As with the other validation experiments, it'd be nice to get some external validation or some error analysis. I don't know if dbSNP's rsID mappings are different from clinvar or if they use a different method. Maybe that'd be a cool experiment too.
Acceptance Criteria
A script to get all dbSNP data, extract all cases of multiple NC expressions across accession versions, extract the chromosomes/positions from them, feed those through agct, aggregate counts of agreement/disagreement, and log cases of concordance.
I don't think this necessarily should be a standard test case (although I bet the stripped-down expressions file might be small enough to check in?) but it'd be nice to have under analysis/ as something we could run occasionally, maybe with a notebook write-up. (language copied from previous tickets)
Proposed solution
No response
Alternatives considered
No response
Implementation details
No response
Potential Impact
No response
Additional context
No response
Contribution
Yes, I can create a PR for this feature.