Question

How to get coordinates from HGVSc, HGVSp and gene name

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6.5 years ago

Korsocius ▴ 250

Dear all, I have table with 3 columns (tab separated). HGVSc, HGVSp, GENE NAME. I need to get coordinates for this rows. Which database I need to download via ftp, to join it together and get what I want please? Thank you

next-gen hgvs • 5.2k views

ADD COMMENT • link updated 6.5 years ago by Emily 23k • written 6.5 years ago by Korsocius ▴ 250

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Hello,

whatever program you use to solve your task, be aware that the combination HGVS/Gene without a transcript could be ambiguous .

fin swimmer

ADD REPLY • link 6.5 years ago by finswimmer 16k

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Please post few examples here.

ADD REPLY • link 6.5 years ago by cpad0112 21k

score 2 · Accepted Answer · 2017-10-10

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6.5 years ago

Emily 23k

You could put the HGVSc notation into the Ensembl VEP.

ADD COMMENT • link 6.5 years ago by Emily 23k

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Right, thank you...I forgot I have local installation of ensembl on my PC, but I have to actualize it. So I could use some Querry. Thank you so much.

ADD REPLY • link 6.5 years ago by Korsocius ▴ 250