Question: Ensembl VEP cannot parse HGVS notation.
0
gravatar for gmora
3.4 years ago by
gmora20
gmora20 wrote:

Hello.

So I used VEP to analyze ENST to refseq transcripts in terms of position differences between them. However when I run my HGVS notations through VEP I get these errors (for HBA1 gene, if that helps).

WARNING: Unable to parse HGVS notation 'ENST00000320868:c.-52C>T'

WARNING: Unable to parse HGVS notation 'ENST00000320868:c.-42C>T'

All of the other HGVS work in the file. I'm curious as to why this is occuring, furthermore I have noticed in happen in some other files but not all.

Any insight would certainly be appreciated! :)

parsing ref_seq vep ensembl hgvs • 1.2k views
ADD COMMENTlink modified 13 months ago by zx87548.2k • written 3.4 years ago by gmora20
1
gravatar for gmora
3.4 years ago by
gmora20
gmora20 wrote:

Solved it appears as though the ENST transcript have slightly different naming conventions for variants in the UTR regions.

ADD COMMENTlink written 3.4 years ago by gmora20
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