# Harmonization by effect allele using gentropy

**URL:** https://community.opentargets.org/t/harmonization-by-effect-allele-using-gentropy/1753
**Category:** Technical Support
**Created:** [7 April 2025 16:05 UTC](https://community.opentargets.org/t/harmonization-by-effect-allele-using-gentropy/1753 "2025-04-07T16:05:34Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![abhukku](https://avatars.discourse-cdn.com/v4/letter/a/8dc957/32.png) [@abhukku](https://community.opentargets.org/u/abhukku)
#### Post date: [7 April 2025 16:05 UTC](https://community.opentargets.org/t/harmonization-by-effect-allele-using-gentropy/1753/1 "2025-04-07T16:05:34Z")

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Hello!

I had a question about the harmonization script within gentropy. Is the harmonization by effect allele (i.e. flipping effect allele/effect size of the variant when necessary) inherent to this script, or is it assumed that it is done before this script is run?

Thank you!

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### Author: ![Prashant\_Uniyal](https://dub1.discourse-cdn.com/flex017/user_avatar/community.opentargets.org/prashant_uniyal/32/382_2.png) [@Prashant\_Uniyal](https://community.opentargets.org/u/Prashant_Uniyal)
#### Post date: [14 April 2025 08:59 UTC](https://community.opentargets.org/t/harmonization-by-effect-allele-using-gentropy/1753/2 "2025-04-14T08:59:24Z")

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Hi @abhukku ,

The harmonisation is performed by GWAS Catalog and FinnGen before Gentropy. As Open Targets ingests credible sets from them, they are not harmonised by us.  
For UKBB-PPP, Open Targets performed the harmonisation.  
Everything is harmonised on GnomAD reference.

Hope this helps.

Best,  
Prashant