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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.

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  • $\begingroup$ VCF files contain information on variants. Each position in a VCF file can be attributed to a gene (if it falls within a gene), is that what you're looking for? By "gene annotation of the already existing reference genome", are you referring to a GTF/GFF file? $\endgroup$
    – Ram RS
    Feb 24 '20 at 18:51
  • $\begingroup$ I believe the question is about using VEP. ensembl.org/info/docs/tools/vep/index.html maybe? $\endgroup$ Feb 24 '20 at 19:33
  • $\begingroup$ People should really stop abusing the word "convert". Does OP wish to annotate their VCF or query a larger dataset based on some data in the VCF or do they think they can actually convert information about variants to information about genes? $\endgroup$
    – Ram RS
    Feb 24 '20 at 20:46
  • $\begingroup$ I already have annotate my VCF(actually bcf file) file with SnpEff. So I sort of doubt whether it was possible to convert it to information about genes. On one hand it would be logically if it could on a biological perspective, on a technical perspective however, it wouldn't be that strange it that isn't that easy. $\endgroup$ Feb 25 '20 at 10:23
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    $\begingroup$ Yes I think I need VEP $\endgroup$ Feb 25 '20 at 10:24
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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.

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