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vcf file from gene name and amino acid change

Hi

How can I generate a VCF file from the gene name and amino acid change for hg19?

for example starting from EGFR p.L858R...

Thanks and best

Verena

vcf
• 2,847 views • link
updated by finswimmer finswimmer • written by v4tischler • v4tischler
  1. Why do you wish to do this?
  2. What have you tried?
  3. You realize this will be a one line VCF with a header much larger than the actual entry?
• 0 views • link
written by Ram Ram

Hi RamRS I have a list (appr. 300 variants) with only this information and need the vcf file for further analysis looked for programs and tools but did not find what I am looking for this information is needed (minimum requirements)

CHROM POS ID REF ALT
1 910438 . A G

Thanks and best,

Verena

• 0 views • link
updated by Ram Ram • written by v4tischler • v4tischler

What sort of downstream analysis are you looking at? You're going from less information content -> more information content, which means you will be using dummy placeholder data for any analysis that absolutely needs a VCF file. OTOH, if it only needs a tab-separated file of coordinates and alleles, the tool will not need a VCF file.

• 0 views • link
written by Ram Ram

2 answers

Goto ensembl's VEP and paste your variant description in the format

EGFR:p.L858R

You can download the result in vcf format.

Please notice that you provide an amino acid change without a transcript name. This can lead to ambiguous results, because

  • each of the 3 bases of a triplet might lead to a different amino acid of its changed.
  • Genes can have multiple transcripts. The the position of the amino acid itself can be ambiguous.

fin swimmer

• 0 views • link
written by finswimmer finswimmer

Hi RamRS

  1. I have a list (appr. 300 variants) with only this information and need the vcf file for further analysis
  2. looked for programs and tools but did not find what I am looking for
  3. this information is needed (minimum requirements)
    CHROM  POS     ID      REF     ALT     
    1       910438  .       A       G

Thanks and best,

Verena

• 0 views • link
updated by Ram Ram • written by v4tischler • v4tischler

Hi v4tischler ,

This reply is better suited as a reply to my comment. Could you make the appropriate change please? That would involve the following steps:

  1. Copy the contents of your reply from this answer (you can edit this answer (Ctrl/Cmd + click the link to open it in a new tab) and do a Select All -> Copy there).
  2. Click on Add Reply on my comment here: C: vcf file from gene name and amino acid change
  3. Paste the copied text
  4. Click on the green Add Comment button
  5. Click on moderate back in your answer here: A: vcf file from gene name and amino acid change
  6. Choose Delete Post
  7. Click on the blue Submit button.

Thank you!

P.S: Please do not add answers unless you're answering the top level question. Use Add Comment or Add Reply as appropriate.

• 0 views • link
written by Ram Ram

Once you move your content to a reply, we can continue this discussion.

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written by Ram Ram

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