Documentation Status Install with Bioconda Available on Galaxy

CrossMap

CrossMap is a command-line tool for converting genomic coordinates, annotation files, and sequencing alignments between genome assemblies using UCSC chain files.

CrossMap supports many commonly used genomics file formats, including

  • BED

  • GFF/GTF

  • VCF

  • BAM/CRAM

  • BigWig

  • Wiggle

  • BEDGraph

Installation

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

Documentation

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 or later (GPL-3.0-or-later).

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for liguow from gravatar.com liguow

Credits

Author: Liguo Wang

License

GNU General Public License v3 or later (GPLv3+) (CrossMap is a program for converting genome coordinates between different)

Requires

Python >=3.8

Provides Extra

docs

Tags

genome genomics liftover bioinformatics assembly

Classifiers

Report project as malware

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