recipe somaticseq

An ensemble approach to accurately detect somatic mutations

Homepage:

http://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:

3.7.3-0,  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, 

3.7.3-0,  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

• gatk4

• lofreq

• muse

• numpy

• pandas

• pysam

• python >=3

• r-ada

• r-base

• scalpel

• scipy

• vardict

• varscan >=2

• xgboost

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install somaticseq

and update with:

conda update somaticseq

or use the docker container:

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

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

Download stats

Link to this page

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