liftover is performed using 1-based coordinates against a 0-based chain file #52
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Hello all!
as descrobed in the title - we believe there is a bug due to the disconnect between 1-based gneome coordinates and 0-based chain files by pyliftover (chain files from the LiftOver tool from pyliftover: https://github.com/EBISPOT/gwas-sumstats-harmoniser/blob/master/harmoniser/map_to_build.py#49)
This diagram walks through the effects of incorrectly passing the 1-based coordinates (lines 2 and 3) versus the actual genomic change between the builds (line 1) and the correct output produced by passing the 0-based coordinate (line 4):
Credit to @katiedelange :)