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