The DAG for harmonisation and fine-mapping of UKBB-PPP

[addramir]

The closest to finish DAG. Includes steps for harmonisation, locus breaker and collection.

• [x] Add the step for locus breaker and locus collection - Step is called: LocusBreakerClumpingStep
• [ ] Modify the fine-mapper step here - https://github.com/opentargets/gentropy/pull/764
• [x] Lets keep postprocessing here. https://github.com/opentargets/gentropy/blob/dev/src/gentropy/credible_set_qc.py

[project-defiant]

Linking current DAGs:

• harmonisation
• fine-mapping done by Kirill

@addramir to clear it up from the DAG perspecive:

• [ ] add LocusBreakerClumpingStep to the harmonisation dag
• [ ] add qc step to inform which loci should be filtered out - this should create a loci manifesto like one in gs://genetics-portal-dev-analysis/dc16/output/ukb_ppp/clean_loci.parquet
• [ ] merge finemapping dag to harmonisation
• [ ] rename the harmonisation dag to ukb_ppp_eur_ingestion

[addramir]

Not sure whether merge finemapping dag to harmonisation is a good idea. The data is hamronised and unlikly to be changed but we may want to rerun FM several times with diffrent parameters.

[project-defiant]

Even if the dags are merged, starting from the finemapping is just commenting the config.

[addramir]

Ok, sounds good. Do you need any help here?

[project-defiant]

Just point me to the QC step