Ask for a tools which can mirror the result of FastaAlternateReferenceMaker to an annotation file
I have identified ~5000 genetic variants including SNPs, deletions, and indels in my yeast strain compared to s288c. Using FastaAlternateReferenceMaker, I made a new consensus sequence by incorporating all variants written in the VCF file. Also, I want to change my annotation file (gff) as well because the indels changed the original genome position. Does anyone know any tools such that I can change my annotation file corresponding to the generated consensus sequence? Thank you for your kind support.
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