text: user6573: 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.
  
  user650: 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.
  
original_text: 6573: <p>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.</p>
   650: <p>Creating a FASTA file by applying variants found in a VCF file is called "creating a consensus FASTA file". You can use <a href="https://samtools.github.io/bcftools/bcftools.html#consensus" rel="nofollow noreferrer"><code>bcftools consensus</code></a>. 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.</p>
  
  <p>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 <a href="https://hgvs.readthedocs.io/en/stable/" rel="nofollow noreferrer">the hgvs python module</a> works well with the HGVS notation, but I don't see a way to "apply" the variant to the reference sequence.</p>
  