recipe somaticseq

An ensemble approach to accurately detect somatic mutations

Homepage:

https://bioinform.github.io/somaticseq/

License:

BSD / BSD-2-Clause

Recipe:

/somaticseq/meta.yaml

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:

3.8.0-0,  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, 

3.8.0-0,  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 bedtools:

depends gatk4:

depends lofreq:

depends muse:

depends numpy:

depends pandas:

depends pydantic:

depends pysam:

depends python:

>=3

depends r-ada:

depends r-base:

depends scalpel:

depends scipy:

depends vardict:

depends varscan:

>=2

depends xgboost:

>=1.4

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install somaticseq

and update with::

   mamba update somaticseq

To create a new environment, run:

mamba create --name myenvname somaticseq

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/somaticseq:<tag>

(see `somaticseq/tags`_ for valid values for ``<tag>``)

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