CrossMap is a command-line tool for converting genomic coordinates, annotations, and sequencing alignments between genome assemblies using chain files.
CrossMap supports many commonly used genomics file formats, including
Install the latest release from PyPI:
pip install CrossMap
Or install the latest development version from GitHub:
pip install git+https://github.com/liguowang/CrossMap.git
https://crossmap.readthedocs.io/
https://github.com/liguowang/CrossMap
Convert a BED file from hg19 to hg38:
CrossMap bed \ hg19ToHg38.over.chain.gz \ input.bed \ output.bed
CrossMap is distributed under the GNU General Public License v3.0 or later (GPL-3.0-or-later).
If you use CrossMap in your research, please cite:
Zhao H, Sun Z, Wang J, Huang H, Kocher J-P, Wang L. CrossMap: a versatile tool for coordinate conversion between genome assemblies Bioinformatics. 2014;30(7):1006–1007.