Closed jonathangriffiths closed 1 year ago
Hey Jonny, thank you very much for this, it is a great help that is much appreciated! I will merge this with the master branch (dev version). The only change I will make is to remove the UCSC chain files from the package and just add a parameter so users can point to them if they are downloaded or download them directly from UCSC otherwise. I think this will avoid the licensing issues. I will however set the default to use the Ensembl versions by default, I understand there could be differences but I don't think we can say one is the 'right' choice over another. Just mentioning the related issue: https://github.com/neurogenomics/MungeSumstats/issues/128
Nice work with this package - it is extremely useful.
As you've noted, the UCSC chain files require a licence for commercial use. Fortunately, Ensembl also provide chain files. The changes I have made allow use of the Ensembl chain files for liftOver.
I haven't done two things:
Let me know what you think!
Jonny.