.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH FLATTENGTF "1" "February 2020" "flattenGTF 2.0.0+dfsg-1~bpo10+1" "User Commands"
.SH NAME
flattenGTF \- Flatten features included in a GTF annotation and save the modified annotation \
to a SAF format file.
.SH USAGE
.PP
flattenGTF [options] \fB\-a\fR <input_file> \fB\-o\fR <output_file>
.PP
## Mandatory arguments:
.TP
\fB\-a\fR <file>
Name of an annotation file in GTF/GFF format.
.TP
\fB\-o\fR <file>
Name of output file.
.PP
## Optional arguments:
.TP
\fB\-t\fR <string>
Specify feature type in a GTF annotation. 'exon' by default.
Features with the specified feature type are extracted from the
annotation for processing.
.TP
\fB\-g\fR <string>
Specify attribute type in GTF annotation. 'gene_id' by default.
This attribute type is used to group features into metafeatures.
.TP
\fB\-C\fR
Merging overlapping exons into multiple non\-overlapping exons but
all the edges are kept.