recipe biopet-seattleseqkit

#### Tool - Filter This tool can filter a seattle seq file.

Homepage

https://github.com/biopet/seattleseqkit

License

MIT

Recipe

/biopet-seattleseqkit/meta.yaml

#### Tool - Filter

This tool can filter a seattle seq file. A given bed file will only select variants inside this regions. Filtering on specific fields is also possible.

#### Tool - MergeGenes

This tool can merge gene counts from the filter step into 1 combined matrix. Genes that are not there will be filled with 0.

#### Tool - MultiFilter

This tool can filter a seattle seq file. A given bed file will only select variants inside this regions. Filtering on specific fields is also possible.

For documentation and manuals visit our github.io page: https://biopet.github.io/seattleseqkit

package biopet-seattleseqkit

(downloads) docker_biopet-seattleseqkit

Versions

0.2-00.1-0

Depends
Required By

Installation

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

conda install biopet-seattleseqkit

and update with:

conda update biopet-seattleseqkit

or use the docker container:

docker pull quay.io/biocontainers/biopet-seattleseqkit:<tag>

(see biopet-seattleseqkit/tags for valid values for <tag>)

Notes

biopet-seattleseqkit 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-seattleseqkit'. 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-seattleseqkit -Xms512m -Xmx1g'.