Is there some tool that will convert a vcf/bcf file to some gene annotation, based on the fact that I have the gene annotation of the already exsisting reference genome. Or some tool that will give me the genes based on the most probable chance.
Creating a FASTA file by applying variants found in a VCF file is called "creating a consensus FASTA file". You can use
bcftools consensus. Unfortunately, the tools only works genome-wide (at the FASTA level), so you might need to use a different tool to extract a gene sequence from the FASTA file using the gene's co-ordinates.
If the VCF file is annotated with HGVS notations for the variants, there might be a way to use those notations to apply the edit to the reference gene/transcript sequence directly. I know the hgvs python module works well with the HGVS notation, but I don't see a way to "apply" the variant to the reference sequence.