This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to get SNP annotation with 3-letter amino acid abbreviation?

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
• 3,677 views • link
written by jinxinhao1988 jinxinhao1988

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

• 1 views • link
written by finswimmer finswimmer

3 answers

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

• 1 views • link
written by finswimmer finswimmer

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

• 1 views • link
written by jinxinhao1988 jinxinhao1988

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

• 0 views • link
written by jinxinhao1988 jinxinhao1988

You're very welcome.

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

fin swimmer

• 0 views • link
written by finswimmer finswimmer

Thank you.@finswimmer

• 1 views • link
written by cpad0112 cpad0112

update:

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

• 1 views • link
written by jinxinhao1988 jinxinhao1988

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

• 1 views • link
written by NB NB

Log in to answer this question.

More posts like this