Get variant position knowing the gene name, base change, and NM#
1
0
Entering edit mode
3.2 years ago
bisansamara ▴ 10

I have a list of > 45 variants. I need to get the exact position of those variants (i.e. chr#:start-end) knowing the gene name affected, base change, and refseqID (NM#) for each variant. Below are few lines as an example of my data:

Gene----------BaseChange----------refseqID

MAN1B1------c.1897G >T------------NM_016219

CRY1----------c.272G >A-------------NM_004075

Some people suggested using MutationTaster to do this, but I couldn't figure out how to use it. Any suggestion on how to use MutationTaster, or any other method to get the variants positions would be highly appreciated.

gene variant genome coordinates • 866 views
ADD COMMENT
1
Entering edit mode
ADD REPLY
3
Entering edit mode
3.2 years ago

use transvar. Convrt your first and second columns to some thing like this:MAN1B1:c.1897G >T and use transvar.

res

ADD COMMENT
0
Entering edit mode

This is super easy! Thanks.

ADD REPLY
0
Entering edit mode

Hello bisansamara,

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

Upvote|Bookmark|Accept

fin swimmer

ADD REPLY
0
Entering edit mode

if you can install transvar on your machine, it would be much easy:

$ tail -n+2 test.txt |transvar canno -l - -g 1 -m 2  --refseq | cut -f1,2,5 | awk '{gsub("[|/(]","\t")}1' |cut --complement -f3,5,7 | tail -n+2

MAN1B1  c.1897G>T   XM_006716945    chr9:g.137107663G>T p.V633L
MAN1B1  c.1897G>T   NM_016219   chr9:g.137108388G>T p.V633F
CRY1    c.272G>A    NM_004075   chr12:g.107005244C>T    p.W91*

input:

$ cat test.txt 
Gene    BaseChange  refseqID
MAN1B1  c.1897G>T   NM_016219
CRY1    c.272G>A    NM_004075

If you want only for the transcripts in the list:

$ tail -n+2 test.txt |transvar canno -l - -g 1 -m 2 -t3 --refseq | cut -f1,2,5 | awk '{gsub("[|/(]","\t")}1' |cut --complement -f3,5,7 | tail -n+2

MAN1B1  c.1897G>T   NM_016219   chr9:g.137108388G>T p.V633F
CRY1    c.272G>A    NM_004075   chr12:g.107005244C>T    p.W91*
ADD REPLY

Login before adding your answer.

Traffic: 2262 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6