Harmonization by effect allele using gentropy

Technical Support
1

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!

2

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