Question: How to retrieve gene annotation "HGVS cDNA" (e.g. c.158G>A) by chromosome position
0
gravatar for merobin8
2.1 years ago by
merobin80
merobin80 wrote:

How can I convert chromosome position (e.g GRCh37/hg19 position,12:103306579 C/T) to HGVS cDNA (e.g c.158G>A) ? Currently I have got the file refGene.txt , and hg19.fasta , I can retrieve relative info like Alleles (ref/alt) , Transcript, sequence etc. But when try to calculate the position of HGVS cDNA which is 158 , I find my result doesn't match . Can anyone tell me how to caculate the postion in HGVS cDNA ?

sequencing gene • 863 views
ADD COMMENTlink written 2.1 years ago by merobin80
1
gravatar for cpad0112
2.1 years ago by
cpad011213k
India
cpad011213k wrote:
http://grch37.rest.ensembl.org/vep/human/hgvs/12:g.103306579C>T?content-type=application/json;hgvs=1

using Ensembl grch 37 rest api and final format is in json format. Filter by hgvsc (ENST00000553106.1:c.158G>A)

If you parse the json for hgvsc and hgvsp, you would some thing like this:

ENST00000307000.2:c.143G>A  ENSP00000303500.2:p.Arg48His
ENST00000546844.1:c.158G>A  ENSP00000446658.1:p.Arg53His
ENST00000548677.1:n.245G>A  
ENST00000548928.1:n.80G>A   
ENST00000549111.1:n.254G>A  
ENST00000550978.1:n.142G>A  
ENST00000551337.1:c.158G>A  ENSP00000447620.1:p.Arg53His
ENST00000551988.1:n.247G>A  
ENST00000553106.1:c.158G>A  ENSP00000448059.1:p.Arg53His
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by cpad011213k

Thank you for your suggestion. This will save me a lot of effort , but is it possible to make it localized ? I mean we won't have to rely on the interfaces provided by the third party and produce the result by our own, since it may not be available in the future .

ADD REPLYlink written 2.1 years ago by merobin80

one of the easy to use and offline setup tools is transvar (IMO). If you want offline HGVS translation, you need to download and set up appropriate genome files and annotation files.

ADD REPLYlink written 2.1 years ago by cpad011213k

Yes, you can install a local cache of the VEP data and run it from the command line.

ADD REPLYlink written 2.1 years ago by Emily_Ensembl21k
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