The General Feature Format is a textual format for describing annotations on biological sequences. The format is specified by the Sanger Center at GFF (General Feature Format) Specifications Document.

We assume that the reader is familiar with the GFF record format as described in the above, as we do not repeat this information here. A compliant GFF file for Caryoscope consists of a list of GFF records organized into three consecutive sections:

The sections may not be interspersed or reordered. For each section, we define the interpretation of each record belonging to that section below.

Caryoscope accepts text files in comma- or tab-delimited format, as are usually exported or imported by popular spreadsheet software. Caryoscope expects the columns in these files in a format very similar to the GFF file described in Section 3.4.1, “General Feature Format”.

A compatible text file has three sections, as does the GFF case, for chromosomes, centromeres and features, respectively. Some columns are mandatory, as described below, while further columns to the right are considered annotations, and are treated in the same way that the "<attributes>" field is used in the GFF case.