[svtoolkit-help] Gene Overlap Annotator

[Markus S. A. <mar...@im...>]

Hi,
I have used the deletion pipeline and would now like to use the Gene Overlap Annotator to classify my deletions. This is a non-human organism so I need to use my own GTF annotation file, which do not work as it is even if it is pretty similar to GENCODEs GTF.
The specifications for this file is not clear to me, including the sort order. Also, the link to the SortGTFFile utility in the documentation seems dead.

Could you please provide some clearer specifications of the GTF file and information about
SortGTFFile?

Best,
Markus