Question

Getting CDS from chromosome positions

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5.1 years ago

drmouradap • 0

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.

sequence cds genome browser chromosome position • 1.2k views

ADD COMMENT • link updated 5.0 years ago by Luis Nassar ▴ 670 • written 5.1 years ago by drmouradap • 0

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

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

ADD REPLY • link 5.1 years ago by Pierre Lindenbaum 164k

score 0 · Answer 1 · 2019-10-30

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5.1 years ago

JC 13k

You can use Ensembl VEP API

ADD COMMENT • link 5.1 years ago by JC 13k

score 0 · Answer 2 · 2019-12-11

The UCSC Genome Browser may not be the most efficient tool to go from position coordinate to predicted effect via programmatic approach.

We recently announced our API (http://genome.ucsc.edu/goldenPath/help/api.html) which does allow python access to coding sequence given coordinates, as well as querying most of the available data (among other functions). Hopefully that will be of some use.