Change VCF File Reference Genome to a Local .FA File

Question

[Arda]

I have a single chromosome VCF file that I want to align to a chromosome sequence I have locally in a .fa file, is it possible to convert the VCF file so its reference genome is the sequence I have on my .fa file. If so, how could this be achieved.

[GenoMax]

Not completely certain what you are asking but this will likely help: https://gatk.broadinstitute.org/hc/en-us/articles/360037594571-FastaAlternateReferenceMaker

[WouterDeCoster]

So you mean that the VCF was generated by alignment to another reference genome, and now you want to update the coordinates to a new reference genome? If so, the command you are searching for is liftover, available from Picard (and others)