Question: Getting CDS from chromosome positions
0
gravatar for drmouradap
5 weeks ago by
drmouradap0
drmouradap0 wrote:

Hello! I'm sorry if this is a duplicate question. I've searched the forum and didn't find the answer to what I seek.

I'm working with exome sequencing data and some of the variants are not completely annotated. I have the chromosome positions of each variant, but not the CDS or protein change associated with it.

My question is how to extract the CDS from the chromosome positions of each variant, to translate these variants into Synonymous/Non-Synonymous variations and then get the predicted protein effects of each variant. I thought of using UCSC Genome Browser for that. I there an easy way to extract that information using Python?

Example: I want to get from chr9:34371171 T>C to c.T1773C / p.I591T.

ADD COMMENTlink modified 5 weeks ago by JC9.1k • written 5 weeks ago by drmouradap0
2

. I've searched the forum and didn't find the answer to what I seek.

Tool for CDS Variants annotation : snpeff, vep, annovar, ...

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Pierre Lindenbaum124k
0
gravatar for JC
5 weeks ago by
JC9.1k
Mexico
JC9.1k wrote:

You can use Ensembl VEP API

ADD COMMENTlink written 5 weeks ago by JC9.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2269 users visited in the last hour