BamSnap

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

For more details, see BamSnap Documentation.

Modification

I updated the code to compatible with CIGAR string with tag 3 (skipped region from the reference). I also upload corresponding docker image to dockerhub.

Installation

Prerequisites

• python 3.4+
• Pillow (Python Imaging Library)
• pysam
• pyfaidx
• pytabix

Install with github

git clone https://github.com/shengqh/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 shengqh/cqs_bamsnap
$ docker run --rm -it -v /local_directory_path:/directory_path_in_image shengqh/cqs_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