Create naive variation search

GenomicMedLab / gregor

Handle GREGoR Consortium tasks/code

MIT License

0 stars 0 forks source link

Create naive variation search #7

Open jsstevenson opened 2 months ago

jsstevenson commented 2 months ago

Index VRS IDs for called variants to participant_id

[ ] Define workflow to gather all annotated VCFs and produce some index/output
[ ] Decide on the format of that index (literal index file, DB upload callback, etc)

Just a literal index file is technically a redundant intermediary step, but does afford some freedom to experiment with outputs. A DB callback might be better although we need to be forward thinking about things like schema.

jsstevenson commented 2 months ago

How to handle position searches when a ref/alt is of length > 1?
How to handle position searches on indels?

ahwagner commented 2 months ago

We want to be able to retrieve all patients with a given variant, specified by VRS ID. I expect we can leverage VRS computed identifiers for rapid querying on an index (existing wherever–parquet, flat file, GREGoR-maintained db, etc.).

At the GREGoR conference this week, I will ask Ben and Marsha about the GREGoR variants browser and if there is a backend and API we may use.