BamSnap¶
BamSnap is a visualization tool for aligned BAM files that allows to generate high-quality snapshots of read level data in high-throughput, processing up to thousands of files. BamSnap is a command-line software based on python.
Setting up BamSnap¶
In a command prompt or terminal window, run the following commands to install and test the software.
$ pip install bamsnap
$ bamsnap -bam test.bam -pos chr1:7364529 -out test.bam.png
More examples and commands are available in gallery. Use -h
to list the options available for bamsnap
.
$ bamsnap -h
Source code is available on github.
Contents¶
- 1. Installation
- 2. Gallery
- 3. Optional arguments
- 4. Input files
- 5. Output files
- 6. Plot options
- 7. Read alignment track (
-bamplot read
) - 8. Coverage track (
-bamplot coverage
) - 9. Base track (
-draw base
,-bamplot base
) - 10. Gene track (
-draw gene
) - 11. Coordinates track (
-draw coordinates
) - 12. Heatmap track (
-bamplot heatmap
) - 13. Version History