Question: How to get SNP annotation with 3-letter amino acid abbreviation?
1
gravatar for jinxinhao1988
4 weeks ago by
China/Beijing
jinxinhao198850 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 • 255 views
ADD COMMENTlink modified 16 days ago • written 4 weeks ago by jinxinhao198850

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 4 weeks ago • written 4 weeks ago by finswimmer2.8k
4
gravatar for finswimmer
4 weeks ago by
finswimmer2.8k
Germany
finswimmer2.8k 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 4 weeks ago by finswimmer2.8k

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

ADD REPLYlink written 4 weeks ago by jinxinhao198850

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

ADD REPLYlink written 4 weeks ago by jinxinhao198850

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 4 weeks ago by finswimmer2.8k

Thank you.@finswimmer

ADD REPLYlink written 29 days ago by cpad01126.4k
1
gravatar for jinxinhao1988
16 days ago by
China/Beijing
jinxinhao198850 wrote:

update:

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

ADD COMMENTlink written 16 days ago by jinxinhao198850
1
gravatar for Nandini
4 weeks ago by
Nandini550
London
Nandini550 wrote:

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

ADD COMMENTlink written 4 weeks ago by Nandini550
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