Question: Retrieve mutation position and ID for a mutation in hgvs format
0
gravatar for vigprasud
3.9 years ago by
vigprasud60
United States
vigprasud60 wrote:

How can I find a mutation's chr pos and id represented in HGVS format?

Eg:  

Gene: TMEM231    cdna_Change: NM_001077418.1:c.582+3A>G    protein_change: p.?

The mutations are represented in HGVS format. How and where can I find the rs#, chr and pos for this particular mutation. 

I have a set of 10000 mutations and would like to annotate then with their chr, pos and rs#

annotation dbsnp mutation hgvs • 5.1k views
ADD COMMENTlink modified 2.6 years ago by Reece250 • written 3.9 years ago by vigprasud60

What programming languages do you know? This could be done in R (and presumably biopython/bioperl) relatively easily.

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by Devon Ryan81k

I know python and R

ADD REPLYlink written 3.9 years ago by vigprasud60
1

If VEP doesn't work for you, then you can do this in R. The general steps would be to:

  1. Load this file as a dataframe and parse the cdna information to split the ID from the position information.
  2. Load a txdb that contains these IDs (they don't all).
  3. You can then just apply a function to each transcript to calculate the cDNA position of each exon (you'd just use the 5' or 3' most coordinate).
  4. Now you have numbers you can compare, so you'll need to apply a function to extract the appropriate transcript and then just determine (A) which exon it would be in (or intron following an exon as in your example) and then (B) increment/decrement the genomic position of said exon by the appropriate offset.
ADD REPLYlink written 3.9 years ago by Devon Ryan81k

The Ensembl VEP should work fine for this, as it does accept HGVS notations on RefSeq transcripts as input. No need for any programming. The documentation for the VEP is excellent!

ADD REPLYlink written 3.9 years ago by Bert Overduin3.6k
6
gravatar for Jeremy Leipzig
3.9 years ago by
Philadelphia, PA
Jeremy Leipzig17k wrote:

I would try VEP:

http://uswest.ensembl.org/Homo_sapiens/Tools/VEP

 

 

ADD COMMENTlink written 3.9 years ago by Jeremy Leipzig17k

I second VEP, it works quite well for this. I forget what the limit is for the number of variants through the online web interface but you can either do it that way in batches or do it through the command-line version. You just have to switch from the default and you can put in HGVS mutations using RefSeq sequences

ADD REPLYlink written 3.9 years ago by Dan Gaston7.0k

Thank you. That helps.

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by vigprasud60
1
gravatar for Vivek
3.9 years ago by
Vivek2.1k
Denmark
Vivek2.1k wrote:

The lesser mentioned yet totally awesome webpage, https://mutalyzer.nl/positionConverter

ADD COMMENTlink written 3.9 years ago by Vivek2.1k

I see that mutalyzer works for converting rsIDs to HGvs but not the other way around.

ADD REPLYlink written 15 months ago by Ritika0
0
gravatar for Reece
2.6 years ago by
Reece250
United States
Reece250 wrote:

Also consider the Python hgvs package[Disclosure: I'm one of the authors.]

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Reece250
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