UCSC parameters for converting between human genome builds

Question

[jon.klonowski]

I am honestly surprised this hasnt been discussed here before. Maybe I am missing the post. What are the ideal parameters for UCSC LiftOver when doing a simple conversion between human genome builds (i am interested in hg18 to hg38 but I imagine that the parameters for this would also be ideal for conversion between other human genome builds). I am feeding LiftOver a whole exome sequencing design file (.bed interval file of theoretical sequencing targets).

Specifically:

1. "Minimum ratio of bases that must remap:" I saw someone said the use 0.9 for within species conversions.
2. "Allow multiple output regions: " Is this a no? (why?)
3. Any other parameters should/could be changed?