Has anybody had any success with any tools other than LiftOver or NCBI's Genome Remapping Service for mapping/translating reference genome positions? My experience with LiftOver has been less than satisfactory and NCBI does not seem to offer any local version of their tool. Other than BLASTing every sequence I have against a full-genome database, are there any accurate alternatives?
I recently put up https://liftover.broadinstitute.org/ to make it a little easier to check liftover coords for specific variants or intervals. It takes fewer clicks and supports more input formats than UCSC liftover and Assembly Converter.
You should give pslMap from the UCSC tools collection a try. It's different that it not only lifts the ends of the regions.
If you don't have enough recovery, you should lower the minMatch parameter. By default it's set to 0.95 which might be too high for non-human liftovers. If there is a good alignment, liftOver will use it. We would need an example to find out why your region did not lift.