What are currently the best tools for lifting over genome coordinates from one custom genome build to another custom genome build.
I found this 4 year old post that mentions UCSC liftOver as the top tool but that seems to be limited to model organisms as you need the chain file from UCSC . I can't find anywhere how to create these chain files your self: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)
Is it possible to create these UCSC liftOver chain files by your self for custom genome builds?
Are there other tools with the same quality and functionality as UCSC liftOver that support creating these "chain" files yourself for custom reference genomes? How difficult and time / resource consuming is it to build these chain files?
Do these chain files and the lift over process take strand into account? If I have a VCF with an A/T SNP positions do they flip it to T/A SNP position if the new reference genome has a genome region flipped to the different DNA strand?
Does lift over support INDEL variants?