agat/agat_convert_sp_gff2gtf

gene annotations

GTF conversion

Description

The script aims to convert any GTF/GFF file into a proper GTF file. Full
information about the format can be found here:
https://agat.readthedocs.io/en/latest/gxf.html You can choose among 7
different GTF types (1, 2, 2.1, 2.2, 2.5, 3 or relax). Depending the
version selected the script will filter out the features that are not
accepted. For GTF2.5 and 3, every level1 feature (e.g nc_gene
pseudogene) will be converted into gene feature and every level2 feature
(e.g mRNA ncRNA) will be converted into transcript feature. Using the
"relax" option you will produce a GTF-like output keeping all original
feature types (3rd column). No modification will occur e.g. mRNA to
transcript.

To be fully GTF compliant all feature have a gene_id and a transcript_id
attribute. The gene_id is unique identifier for the genomic source of
the transcript, which is used to group transcripts into genes. The
transcript_id is a unique identifier for the predicted transcript, which
is used to group features into transcripts.

Type

bash_script

License

GPL-3.0

Keywords

gene annotations

GTF conversion

Links

Repository

Issues

Documentation

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.gtf"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/biobox.git \  
  -revision v0.4.0 \  
  -main-script target/nextflow/agat/agat_convert_sp_gff2gtf/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--gff -i	file required	Input GFF/GTF file that will be read

Name

Type & Properties

--gff

-i

file

required

Outputs

Name	Type & Properties	Description
--output -o --out --outfile --gtf	file required output	Output GTF file. If no output file is specified, the output will be written to STDOUT.

Name

Type & Properties

--output

-o

--out

--outfile

--gtf

file

required

output

Arguments

Name	Type & Properties	Description
--gtf_version	string	Version of the GTF output (1,2,2.1,2.2,2.5,3 or relax). Default value from AGAT config file (relax for the default config). The script option has the higher priority. * relax: all feature types are accepted. * GTF3 (9 feature types accepted): gene, transcript, exon, CDS, Selenocysteine, start_codon, stop_codon, three_prime_utr and five_prime_utr. * GTF2.5 (8 feature types accepted): gene, transcript, exon, CDS, UTR, start_codon, stop_codon, Selenocysteine. * GTF2.2 (9 feature types accepted): CDS, start_codon, stop_codon, 5UTR, 3UTR, inter, inter_CNS, intron_CNS and exon. * GTF2.1 (6 feature types accepted): CDS, start_codon, stop_codon, exon, 5UTR, 3UTR. * GTF2 (4 feature types accepted): CDS, start_codon, stop_codon, exon. * GTF1 (5 feature types accepted): CDS, start_codon, stop_codon, exon, intron.
--config -c	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 orignal 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).

Name

Type & Properties

--gtf_version

string

--config

-c

file