/bamsnap

Primary LanguageHTMLMIT LicenseMIT

BamSnap

BamSnap: a lightweight command-based visualization tool for sequencing reads in BAM files.

Disclaimer: This is not the official version of bamsnap, but the one adapted for not only human but also Plasmodium species

For more details, see BamSnap Documentation.

Installation

Prerequisites

Install with github

git clone https://github.com/marcguery/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