The script aims to compare two annotation of the same assembly. It provided information about split/fusion of genes between the two annotations. The most common case are: 1 => 0 ( gene uniq to file1) 0 => 1 ( gene uniq to file2) 1 => 1 ( 1 gene from file 1 overlaps only 1 gene from file2) 1 => <many> ( 1 gene from file 1 overlaps <many> genes from file2) => split case (with file 1 as reference) <many> => 1 ( <many> genes from file 1 overlap only 1 gene from file2) => fusion case (with file 1 as reference)
Then you can get more complex cases: <many> => <many> (<many> genes from file 1 overlap <many> genes from file2)
agat_sp_compare_two_annotations.pl -gff1 infile.gff [ -o outfile ] agat_sp_compare_two_annotations.pl --help
Input GTF/GFF file1.
Input GTF/GFF file2.
-o , --output , --out or --outfile
Output GFF file. If no output file is specified, the output will be written to STDOUT.
Verbose option, make it easier to follow what is going on for debugging purpose.
-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 you the possibility to use your own AGAT config file (located elsewhere or named differently).
-h or --help
Display this helpful text.