Exon number of chromosomal position

Question

[gero.knittel]

Hi everybody,

I'm sure this is a very trivial question to many of you, unfortunately not to me, though:

I'm having a list of mutations with their chromosomal positions, and I would need to know in which exons they are. We are designing a targeted sequencing panel and for each of the relevant genes, I would need to know whether the mutations are limited to certain exons, or whether the whole gene has to be sequenced.

Would be great if you could help me withhow to best do this.

Best, and thanks in advance, Gero.

[cpad0112]

Intersect vcf with gtf with exon coordinates.

Answer 1

[finswimmer]

Hello,

ensembl's VEP could do this for you. But be aware that a gene can have multiple transcripts and therefor the result can be ambiguous.

fin swimmer

[gero.knittel]

Thank you, that will do the trick. There's also a bio conductor package for that, great!

[finswimmer]

You're welcome.

You should mark the answer as accepted, so one can easily see that your question is solved.

fin swimmer