Modifying an annotation files after transgene insertion

Question

[Assa Yeroslaviz]

I was wondering if anyone know of a way to modify an annotation file, such as a gtf or gff after the reference genome was inserted with a transgene or other external snippets.

We have a Whole Genome Sequencing project, which was done on yeast genome modified with an insertion at chromosome II. I would like to modify my annotation file ( I have in this case only a gff). We know exactly where the sequence was inserted, so I need to modify the positions of all chromosomal elements from a specific position to the end of this chromosome.

I would appreciate the help, if someone knows of a simple way to do so.

thanks

[ATpoint]

We know exactly where the sequence was inserted, so I need to modify the positions of all chromosomal elements from a specific position to the end of this chromosome.

Probably not a good idea as this would change the coordinates of everything downstream of it on that chromosome with regard to the reference genome, so any external annotation that at some point might be needed would need to be modified in the exact same way, sounds very cumbersome and error-prone. Why not just adding the insert as a separate chromosome.

[Assa Yeroslaviz]

The sequence itself is already inserted into the reference genome. yes this is very cumbersome. The project is all about structural variants and CNV identification. the reason behind it was that it would be more precise to insert the snippet into the genome for the mapping, but unfortunately I now need to shift all the coordinates in the gff file from the insertion position by the length of the insert.

Am I wrong with this assumption? If I use the insert as a separate chromosome, would the structural variants (Indels, SNPs, MNPs) would be shown on the correct genomic locations in the results?