How to get SNP annotation with 3-letter amino acid abbreviation?

Question

[jinxinhao1988]

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:

The results I want is like this:

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

Best wishes,

[finswimmer]

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

Answer 1

[finswimmer]

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

[jinxinhao1988]

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

[jinxinhao1988]

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

[finswimmer]

You're very welcome.

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

fin swimmer

[cpad0112]

Thank you.@finswimmer

Answer 2

[jinxinhao1988]

update:

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

Answer 3

[NB]

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