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 ?
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
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 .
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