Hi.

I have usually been using hg19 reference file from ucsc.

However, ucsc has a prefix 'chr' in its files.

Of course, I am able to exclude 'chr' prefix by script programming, but I don't want to.

Instead, I need another human reference file which does not contain 'chr' prefix itself.

Do any another reference files exist not ucsc?
It's never as simple as "remove chr-prefix with a script". [hg19](http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&chromInfoPage=true) is UCSC's variant of the official [GRCh37](https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.13) assembly. Early releases of GRCh37 like [GRCh37-lite](ftp://ftp.ncbi.nlm.nih.gov:/genomes/archive/old_genbank/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37/special_requests/), did not use chr-prefixes, but newer releases like [GRCh37.p13](ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_genbank/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh37.p13/seqs_for_alignment_pipelines/) adopted the chr-prefix, and use a newer mitochondrial (`MT`) sequence than hg19 does. Note also how `chrM` in hg19 is named `MT` in GRCh37. And all the unplaced contigs have very different names. So simply removing the chr-prefix in hg19 does not make it GRCh37. It makes it a wholly other chromosome naming convention, which is the last thing we need right now, since everyone has agreed to use chr-prefixes in GRCh38/hg38, except Ensembl.

**Update (Nov 4, 2016):** [Here is a UCSC Chain](https://github.com/mskcc/vcf2maf/blob/v1.6.15/data/hg19_to_GRCh37.chain) mapping UCSC's hg19 to Ensembl's GRCh37.p13 (no chr-prefix), compatible with tools like [CrossMap](http://crossmap.sourceforge.net), [Remap](https://www.ncbi.nlm.nih.gov/genome/tools/remap/docs/api), or [liftOver](https://genome.ucsc.edu/cgi-bin/hgLiftOver). Notice how all chromosomes/contigs except `chrM` only require renaming. Users of [vcf2maf](https://github.com/mskcc/vcf2maf) with hg19 VCFs as input, can pass this into the `--remap-chain` argument.