recipe gatk4

Genome Analysis Toolkit (GATK4)

Homepage

https://www.broadinstitute.org/gatk/

Developer docs

https://github.com/broadinstitute/gatk

License

BSD / BSD-3-Clause

Recipe

/gatk4/meta.yaml

package gatk4

Versions

4.1.4.1-1, 4.1.4.1-0, 4.1.4.0-1, 4.1.4.0-0, 4.1.3.0-0, 4.1.2.0-1, 4.1.2.0-0, 4.1.1.0-0, 4.1.0.0-0, 4.0.12.0-0, 4.0.11.0-0, 4.0.10.0-0, 4.0.9.0-0, 4.0.8.1-0, 4.0.7.0-0, 4.0.6.0-0, 4.0.5.2-0, 4.0.5.1-0, 4.0.4.0-0, 4.0.3.0-1, 4.0.3.0-0, 4.0.2.1-0, 4.0.2.0-0, 4.0.1.2-0, 4.0.1.1-0, 4.0.1.0-0, 4.0.0.0-0, 4.0b6-0, 4.0b5-0, 4.0b4-0, 4.0b3-0, 4.0b2-0, 4.0b1-0, 4.0a1.2.7.2-2

Depends

• openjdk >=8,<9

• python

Required By

• macaron

• ctat-mutations

• pathogen-profiler

• somaticseq

• tb-profiler

• gatk4-spark

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install gatk4

and update with:

conda update gatk4

or use the docker container:

docker pull quay.io/biocontainers/gatk4:<tag>

(see gatk4/tags for valid values for <tag>)

package gatk4-spark

Versions

4.1.4.1-1, 4.1.4.1-0, 4.1.4.0-1, 4.1.4.0-0, 4.1.3.0-0, 4.1.2.0-1

Depends

• gatk4 4.1.4.1 1

• openjdk >=8,<9

• python

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install gatk4-spark

and update with:

conda update gatk4-spark

or use the docker container:

docker pull quay.io/biocontainers/gatk4-spark:<tag>

(see gatk4-spark/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/gatk4/README.html)