┌┐ ┌─┐┌┬┐┌─┐┌─┐┬  ┬              Quick calculation and visualization
├┴┐├─┤││││  │ │└┐┌┘             of sequence coverage on the terminal
└─┘┴ ┴┴ ┴└─┘└─┘ └┘ v0.1      

Installation

git clone --recurse-submodules https://github.com/fbreitwieser/bamcov
cd bamcov
make
make test

Make sure to clone the repository with --recurse-submodules to get the htslib, otherwise it is necessary to type git submodule update --init --recursive in the cloned repository.

Usage

Show tabular output (default) with header:

./bamcov -H test.bam

Show histogram output:

./bamcov -m test.bam

Show specific region (requires BAM index):

./bamcov -mr NW_002477246.1:1000-200000 test.bam

Use full window width for histogram:

./bamcov -w0 -mr NW_002477246.1:100 test.bam

For high-res mode with 80 steps on the histogram y-axis instead of 20, use the flags -mU. To see if your terminal/font support it check with ./bamcov -v. If the output looks fine without empty blocks, you are good to go to user the -U flag.

Planned features

• BED support
• Show average coverage instead of percent covered in histogram

Please feel free to open an issue with a feature request or comment on an existing one.

Info

This tool is based on htslib and may be integrated in samtools (PR #992). This standalone version will implement new features and will be maintained on its own.

Author: Florian Breitwieser, based on code of samtools depth by Heng Li and samtools contributors.