CrossMap

July 31, 2026 · View on GitHub

CrossMap

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

BED <https://en.wikipedia.org/wiki/BED_(file_format)>/BigBed <https://pmc.ncbi.nlm.nih.gov/articles/PMC2922891/>
GFF/GTF <https://en.wikipedia.org/wiki/General_feature_format>_
VCF/gVCF <https://en.wikipedia.org/wiki/Variant_Call_Format>_
BAM/CRAM <https://en.wikipedia.org/wiki/BAM_(file_format)>_
BigWig <https://pmc.ncbi.nlm.nih.gov/articles/PMC2922891/>_
Wiggle <https://genome.ucsc.edu/goldenpath/help/wiggle.html>_
BeDGraph <https://genome.ucsc.edu/goldenpath/help/bedgraph.html>_

Installation

Install the latest release from PyPI <https://pypi.org/project/CrossMap/>_:

pip install CrossMap

Or install the latest development version from GitHub:

pip install git+https://github.com/liguowang/CrossMap.git

Documentation

https://crossmap.readthedocs.io/ <https://crossmap.readthedocs.io/>_

Source code

https://github.com/liguowang/CrossMap

Example

Convert a BED file from hg19 to hg38:

CrossMap bed
hg19ToHg38.over.chain.gz
input.bed
output.bed

License

CrossMap is distributed under the GNU General Public License v3.0 <https://choosealicense.com/licenses/gpl-3.0/>_ or later (GPL-3.0-or-later).

Citation

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 <https://pmc.ncbi.nlm.nih.gov/articles/PMC3967108/>_ Bioinformatics. 2014;30(7):1006–1007.

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