agat_sp_add_intergenic_regions.pl#
DESCRIPTION#
The script aims to add intergenic features (intergenic_region) to gtf/gff file. The intergenic regions are deduced from gene features (feature type gene from the 3rd column).
SYNOPSIS#
agat_sp_add_intergenic_regions.pl --gff infile --out outFile
agat_sp_add_intergenic_regions.pl --help
OPTIONS#
-
--gff, -f or --ref
Input GTF/GFF file.
-
--out, --output or -o
Output file (default GFF3 - see config to modify output format).
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-c or --config
String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives yo the possibility to use your own AGAT config file (located elsewhere or named differently).
-
-v or --verbose
Add verbosity
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-h or --help
Display this helpful text.