I have a question regarding the parameters available at the command line version but not in R.

Is there a possibility to for example alter the minMatch value (Minimum ratio of bases that must remap)?

Apparently this value adapts automatically from 0.95 default to 0.1 when using a chain for different species (in my case hg19ToMm10.over.chain) in R like it does on the webpage.

Anyways it would be great to manually adjust this value in R.

(I am aware that pslMap is maybe a better idea)

Thanks!

Best wishes,

Nik

I could look into it, but no promises. The rtracklayer liftOver is a complete reimplementation of the UCSC liftover tool, which is only freely available for academic use. I've avoided even looking at the liftover source code.