Export observations from Loqusdb and start annotating variants in Balsamic - Githubissues

Clinical-Genomics / BALSAMIC

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

https://balsamic.readthedocs.io/

MIT License

44 stars 16 forks source link

Export observations from Loqusdb and start annotating variants in Balsamic #1318

Closed ivadym closed 11 months ago

ivadym commented 11 months ago

Need

We would like to start annotating variants in Balsamic using the Loqusdb somatic and germline exported observations.

Suggested approach

A method for annotating variants has been added to Balsamic: https://github.com/Clinical-Genomics/BALSAMIC/issues/1146. The next step is to export germline and somatic variants from their respective databases and start feeding them into the analysis.

Considered alternatives

No response

Deviation

No response

Risk assessment

[ ] Needed
[X] Not needed

Risk assessment link

No response

System requirements assessed

[X] Yes, I have reviewed the system requirements

Requirements affected by this story

No response

Can be closed when

[x] loqusdb-clinical variants exported
[x] loqusdb-somatic variants exported
[x] loqusdb-tumor variants exported

Blockers

Database is currently being filled up.

2023-11-02

loqusdb-somatic: 234 samples
loqusdb-tumor: 271 samples

Anything else?

No response

khurrammaqbool commented 11 months ago

The latest versions of databases are exported to stage. These will be used for validation as well as deployment to production.

Databases	Number of cases	Variants
loqusdb-clinical SNV	10786	273324707
loqusdb-clinical SV	10786	3439616
loqusdb-somstiv SNV	238	1131172
loqusdb-somatic SV	238	562426
loqusdb-germline SNV	275	38209100