bamsnap-cgap 0.3.0

A converter from .bam to .png for specific genomic region.

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 bamsnap

• pypi site for bamsnap

Install 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.png

For 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.png

Example Use Case

• 1000 Genome Data: 1000 genomic loci in 2504 individuals
• BamSnap Plot Gallery