We're currently using a variety of different versions of a variety of different organism reference genomes and are often running into the need to convert between chromosome coordinate naming systems (e.g., when someone wants data aligned against the hg19 reference from ensembl and for a gencode GTF file to be used). This is often as simple as a quick add/remove of "chr", but not always (e.g., who would know that JH806595.1 in gencode is HG1441_PATCH in ensembl?). So, does anyone know of a nice resource somewhere that provides the mappings?
At the end of the day, I just need a tab separated file with the name mappings. I've already written a little python script to perform all of the conversion (a trivial task), but making the mapping files is proving to be a PITA and I assume someone else has already done this.
Edit: BTW, if I have to make the mapping files myself I'll put them on github. It's absurd for that to ever need to be repeated by anyone.
Edit: For what it's worth, at least some of the hg19 gencode<->ensembl mappings are here.