Description

The script aims to remove features based on a kill list. The default behaviour is to look at the features's ID. If the feature has an ID (case insensitive) listed among the kill list it will be removed. /!\ Removing a level1 or level2 feature will automatically remove all linked subfeatures, and removing all children of a feature will automatically remove this feature too.

Input

Name
Description
Pattern

0 ()

1 ()

kill_list (file)

Kill list. One value per line.

*.txt

config (file)

Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the original agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).

*.yaml

Output

Name
Description
Pattern

0 ()

0 ()

Tools

agat Documentation

Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format.

https://github.com/NBISweden/AGATdoi: 10.5281/zenodo.3552717License: GPL v3
Authors