Question: vcf file from gene name and amino acid change
0
gravatar for v4tischler
5 months ago by
v4tischler0
v4tischler0 wrote:

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 • 265 views
ADD COMMENTlink modified 5 months ago by finswimmer11k • written 5 months ago by v4tischler0
  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?
ADD REPLYlink written 5 months ago by RamRS22k

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

ADD REPLYlink modified 5 months ago by RamRS22k • written 5 months ago by v4tischler0

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.

ADD REPLYlink written 5 months ago by RamRS22k
2
gravatar for finswimmer
5 months ago by
finswimmer11k
Germany
finswimmer11k wrote:

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

ADD COMMENTlink written 5 months ago by finswimmer11k
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