vcf file from gene name and amino acid change

Question

[v4tischler]

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

[Ram]

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?

[v4tischler]

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

[Ram]

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.

Answer 1

[finswimmer]

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