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Filter credible sets for 99% during release process #3468

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d0choa opened this issue Sep 16, 2024 · 1 comment · Fixed by opentargets/gentropy#765
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Filter credible sets for 99% during release process #3468

d0choa opened this issue Sep 16, 2024 · 1 comment · Fixed by opentargets/gentropy#765
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d0choa commented Sep 16, 2024 •
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As discussed with @addramir and @DSuveges, we would like to be conservative in the release process and implement a 95% credible set filter during Study Locus validation.

This will imply that a more strict definition of the credible set will be applied to downstream processes (e.g. Colocalisation), and we will only display 95% (more stringent) credible sets in the FE application (cc @gjmcn).

The schemas will remain the same across gentropy + API, and the 99% credible sets will still be available in the staging buckets for future benchmarking exercises.
@d0choa d0choa added Data Relates to Open Targets data team Gentropy labels Sep 16, 2024
@addramir addramir self-assigned this Sep 16, 2024
@d0choa d0choa mentioned this issue Sep 16, 2024
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d0choa commented Sep 17, 2024 •
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A revised decision:

  • PICS will filter for 99%
  • SuSie will produce 99% credible

Validation step:

  • it will annotate the credible sets
  • filter the credible sets for 99%

Subsequent steps:

  • they will not filter the credible sets further

We will not change the schemas now for convenience, but i might be a good thing to revise.

Warning: the current PICS results are already filtered by 95% due to a filter that does not seem to be in the code. Hopefully, this threshold won't be there next time we run PICS

@addramir addramir changed the title Filter credible sets for 95% during release process Filter credible sets for 99% during release process Sep 20, 2024
@addramir addramir removed their assignment Sep 20, 2024
@d0choa d0choa self-assigned this Sep 20, 2024
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feat: 99% credible set validation during study_locus_validation opentargets/gentropy
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