- recipe biopet-bamstats
BamStats is a package that contains tools to generate stats from a BAM file, merge those stats for multiple samples, and validate the generated stats files.
- Homepage:
- License:
MIT
- Recipe:
BamStats is a package that contains tools to generate stats from a BAM file, merge those stats for multiple samples, and validate the generated stats files.
#### Mode - Generate
Generate reports clipping stats, flag stats, insert size and mapping quality on a BAM file. It outputs a JSON file, but can optionally also output in TSV format.
The output of the JSON file is organized in a sample - library - readgroup tree structure. If readgroups in the BAM file are not annotated with sample (`SM`) and library (`LB`) tags an error will be thrown. This can be fixed by using `samtools addreplacerg` or `picard AddOrReplaceReadGroups`.
#### Mode - Merge
This module will merge bamstats files together and keep the sample/library/readgroup structure. Values for the same readgroups will be added. It will also validate the resulting file.
#### Mode - Validate
Validates a BamStats file. If aggregation values can not be regenerated the file is considered corrupt. This should only happen when the file has been manually edited.
For documentation and manuals visit our github.io page: https://biopet.github.io/bamstats
- package biopet-bamstats¶
- Versions:
1.0.1-1,1.0.1-0,1.0-1,1.0-0- Depends:
on openjdk
>=8,<9on python
- Additional platforms:
Installation¶
You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).
Pixi¶
With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:
pixi global install biopet-bamstats
to add into an existing workspace instead, run:
pixi add biopet-bamstats
In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:
pixi workspace channel add conda-forge
pixi workspace channel add bioconda
Conda¶
With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:
conda install biopet-bamstats
Alternatively, to install into a new environment, run:
conda create -n envname biopet-bamstats
with envname being the name of the desired environment.
Container¶
Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:
docker pull quay.io/biocontainers/biopet-bamstats:<tag>
(see biopet-bamstats/tags for valid values for <tag>).
Integrated deployment¶
Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.
Notes¶
biopet-bamstats is a Java program that comes with a custom wrapper shell script. By default 'no default java option' is set in the wrapper. The command that runs the program is 'biopet-bamstats'. If you want to overwrite it you can specify memory options directly after your binaries. If you have _JAVA_OPTIONS set globally this will take precedence. For example run it with 'biopet-bamstats -Xms512m -Xmx1g'.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/biopet-bamstats/README.html)
