- recipe somaticseq
An ensemble approach to accurately detect somatic mutations.
- Homepage:
- Developer docs:
- License:
BSD / BSD-2-Clause
- Recipe:
SomaticSeq is an ensemble caller that has the ability to use machine learning to filter out false positives. The detailed documentation is included in the package, located in docs/Manual.pdf. A quick guide can also be found here. SomaticSeq's open-access paper: Fang LT, Afshar PT, Chhibber A, et al. An ensemble approach to accurately detect somatic mutations using SomaticSeq. Genome Biol. 2015;16:197.
- package somaticseq¶
- Versions:
3.11.1-0,3.11.0-0,3.10.0-0,3.9.1-0,3.8.0-0,3.7.4-0,3.7.3-0,3.7.2-0,3.7.1-0,3.11.1-0,3.11.0-0,3.10.0-0,3.9.1-0,3.8.0-0,3.7.4-0,3.7.3-0,3.7.2-0,3.7.1-0,3.7.0-0,3.6.2-0,3.6.0-0,3.5.1-0,3.5.0-0,3.4.2-0,3.4.1-0,3.4.0-0,3.3.0-0,3.2.1-0,2.8.1-0- Depends:
on gatk4
on lofreq
on muse
on numpy
on pandas
on pybedtools
on pydantic
on pysam
on python
>=3.11on r-ada
on r-base
on scalpel
on scipy
on vardict
on varscan
>=2on xgboost
>=1.4
- 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 somaticseq
to add into an existing workspace instead, run:
pixi add somaticseq
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 somaticseq
Alternatively, to install into a new environment, run:
conda create -n envname somaticseq
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/somaticseq:<tag>
(see somaticseq/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.
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/somaticseq/README.html)
