BamSnap
BamSnap: a lightweight command-based visualization tool for sequencing reads in BAM files
For more details, see BamSnap Documentation.
Installation
Prerequisites
- python 3.4+
- Pillow (Python Imaging Library)
- pysam
- pyfaidx
- pytabix
Install with pip
pip install bamsnapInstall with github
git clone https://github.com/parklab/bamsnap
cd bamsnap
python setup.py install
Usage
Simple usage
$ bamsnap -bam test.bam -pos 1:7364529 -out test.pngFor more details, see BamSnap Documentation.
Usage with docker
$ docker pull danielmsk/bamsnap
$ docker run --rm -it -v /local_directory_path:/directory_path_in_image danielmsk/bamsnap bamsnap \
-bam /directory_path_in_image/test.bam \
-pos 1:7364529 \
-out /directory_path_in_image/test.pngExample Use Case
- 1000 Genome Data: 1000 genomic loci in 2504 individuals
- BamSnap Plot Gallery