liftOver giving error when updating the annotation (gtf/gff)

[everestial]

I am able to run vcf2diploid.jar to create paternal, maternal chain. Then I tried to use these chain to create updated annotation for reference GTF/GFF files. But, I am getting the warning message.

$ liftOver -gff lyrata.Chr2_only.gtf paternal.chain lyrata.Chr2.LiftOv.Paternal.gtf lyrataPaternalNot_lifted.gtf
Reading liftover chains
Mapping coordinates
WARNING: -gff is not recommended.
Use 'ldHgGene -out=<file.gp>' and then 'liftOver -genePred <file.gp>'

[abyzov]

Hi, the warning is related to liftOver tool. Please consult with the corresponding manual. Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic ----------------------------- Mayo Clinic, Harwick 3-12 200 1st street SW, Rochester, MN 55905 tel: +1-(507)-538-0978 fax: +1-(507)-284-0745