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
Source code
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).
1 maintainer
Metadata
1 maintainer
Release files for CrossMap 0.7.4
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| crossmap-0.7.4.tar.gz | 32.9 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| crossmap-0.7.4-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 75.9 kB
Release files / crossmap-0.7.4.tar.gz
| Download URL | crossmap-0.7.4.tar.gz |
|---|---|
| Size | 32.9 kB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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Release files / crossmap-0.7.4-py3-none-any.whl
| Download URL | crossmap-0.7.4-py3-none-any.whl |
|---|---|
| Size | 43.0 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.13.11
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