Question: How to get SNP annotation with 3-letter amino acid abbreviation?
1
gravatar for jinxinhao1988
11 months ago by
China/Beijing
jinxinhao198860 wrote:

Dear all,

Now we used ANNOVAR to annotate our SNP detected. But the result of ANNOVAR is the single-letter Amino acid abbreviation. It's like this: menu_saveimg_savepath20180521134604

The results I want is like this: menu_saveimg_savepath20180521134855

So does anyone knows that which annotation software can feed back this 3-letter amino acid abbreviation? Thanks in advance.

Best wishes,

snp annotation • 676 views
ADD COMMENTlink modified 10 months ago • written 11 months ago by jinxinhao198860

Hello jinxinhao1988,

could you please post/upload an example output file from ANNOVAR so that we can play around with it (An image is quite hard to parse ;) ).

One solution will be to take your language of choice, that can read in your file line-by-line, split it into columns and replace the letters in the HGVS p. column.

fin swimmer

ADD REPLYlink modified 11 months ago • written 11 months ago by finswimmer11k
4
gravatar for finswimmer
11 months ago by
finswimmer11k
Germany
finswimmer11k wrote:

Hello,

assuming that the annovar output file is a tab separated file, here is a python script. Save it as one2three.py and run it like this:

$ python one2three.py annovar.csv > annovar_fixed.csv

fin swimmer

ADD COMMENTlink written 11 months ago by finswimmer11k

Thank you fin. I will try and feed you results.

ADD REPLYlink written 11 months ago by jinxinhao198860

Hello,fin, Thank you for your script, It worked for my results.

ADD REPLYlink written 11 months ago by jinxinhao198860

You're very welcome.

Than please mark my answer as accpeted. So one can see that your problem is solved.

fin swimmer

ADD REPLYlink written 11 months ago by finswimmer11k

Thank you.@finswimmer

ADD REPLYlink written 11 months ago by cpad011211k
1
gravatar for jinxinhao1988
10 months ago by
China/Beijing
jinxinhao198860 wrote:

update:

Actually snpEff can feed back 3-letter Amino acid abbreviation. And the results are quite good.

ADD COMMENTlink written 10 months ago by jinxinhao198860
1
gravatar for Nandini
11 months ago by
Nandini780
London
Nandini780 wrote:

Variant Effect Predictor should be able to give you the 3-letter amino acid abbv as the output.

ADD COMMENTlink written 11 months ago by Nandini780
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