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
  • 1.1. Prerequisites
  • 1.2. Install with pypi
  • 1.3. Install from source
  • 1.4. Install from docker hub
• 2. Gallery
• 3. Optional arguments
  • 3.1. Input files
  • 3.2. Output file
  • 3.3. Plot layout
  • 3.4. Read alignment track
  • 3.5. Base track
  • 3.6. Coverage track
  • 3.7. Heatmap track
  • 3.8. Gene track
  • 3.9. Coordinates track
• 4. Input files
  • 4.1. Alignment file
    • 4.1.1. Input files (-bam for BAM or CRAM format)
      • 4.1.1.1. Title of alignment file(s) (-title)
    • 4.1.2. BAM list file (-bamlist)
  • 4.2. Genomic position
    • 4.2.1. Genomic position (-pos)
    • 4.2.2. VCF file (-vcf)
    • 4.2.3. BED file (-bed)
  • 4.3. Reference sequence file
    • 4.3.1. FASTA file (-ref)
• 5. Output files
  • 5.1. Image file (PNG, JPG)
  • 5.2. Compressed file (-zipout)
  • 5.3. HTML file (index html)
• 6. Plot options
  • 6.1. Plot composition (-draw, -bamplot)
  • 6.2. Plot layout options
• 7. Read alignment track (-bamplot read)
  • 7.1. Layout options
  • 7.2. Read group (-read_group)
  • 7.3. Read color (-read_color_by)
    • 7.3.1. Color by strand (-read_color_by strand)
    • 7.3.2. Color by inter-chromosomal rearrangements (-read_color_by interchrom)
  • 7.4. Show soft clipped part (-show_soft_clipped)
  • 7.5. Deletion
• 8. Coverage track (-bamplot coverage)
• 9. Base track (-draw base, -bamplot base)
  • 9.1. Layout options
  • 9.2. Base track types
• 10. Gene track (-draw gene)
• 11. Coordinates track (-draw coordinates)
  • 11.1. Axis location (-coordinates_axisloc)
• 12. Heatmap track (-bamplot heatmap)
• 13. Version History
  • 13.1. v0.2.x release series
  • 13.2. v0.1.x release series
  • 13.3. Todo