Get VCF-format positions from coding positions

Question

[captainlabman]

How can I get vcf-format positions of genetic variants from coding positions?

I have a large number of variants (100k+) and all of them written as ENST0000003638:c.65G>A, but I need to get vcf-format - 1 3213317 G A (this variant doesn't exist, just example =D ). I'm looking for a way to make a vcf file containing all these variants. Are there any fools for this task?

Answer 1

[Ram]

Use the hgvs python module to go from c_to_g. You might need to make a few changes for it to work with ENSG IDs. You could also use biomaRt.