flattenGTF - toolkit for processing next-gen sequencing data

        This manpage was written by Alexandre Mestiashvili for the Debian distribution and
        can be used for any other usage of the program.

flattenGTF 2.0.3                                   March 2023                                      FLATTENGTF(1)

       flattenGTF Version 2.0.4

              Flatten  features  included  in  a GTF annotation and save the modified annotation to a SAF format
              file.

   Usage:
              ./flattenGTF [options] -a <input_file> -o <output_file>

       ## Mandatory arguments:

       -a <file>
              Name of an annotation file in GTF/GFF format.

       -o <file>
              Name of output file.

       ## Optional arguments:

       -t <string>
              Specify feature type in a GTF annotation. 'exon' by default.  Features with the specified  feature
              type are extracted from the annotation for processing.

       -g <string>
              Specify  attribute  type  in GTF annotation. 'gene_id' by default.  This attribute type is used to
              group features into metafeatures.

       -C     Merging overlapping exons into multiple non-overlapping exons but all the edges are kept.

       flattenGTF - toolkit for processing next-gen sequencing data