Question: ANNOVAR ability to report reference and mutant codon
0
gravatar for dahliashvets
3.8 years ago by
dahliashvets10
United States
dahliashvets10 wrote:

I am curious if anyone knows whether or not ANNOVAR has the ability to report the reference codon and the resulting mutated codon. Annovar includes whether or not the variant results in a synonymous or non-synonymous amino acid change so I would think that there would be an option to report the specific codon change if it occurs. Does anyone know of a command that would accomplish this? Thank you in advance!

 

tool variant codon annovar vcf • 1.3k views
ADD COMMENTlink modified 3.7 years ago by Biostar ♦♦ 20 • written 3.8 years ago by dahliashvets10
1

Yes, it does report the mutated codon as well as amino acid change in case of missense mutations. 

ADD REPLYlink written 3.8 years ago by Ashutosh Pandey11k

Are you able to tell me the actual command that accomplishes this?

ADD REPLYlink written 3.8 years ago by dahliashvets10

The default command (sth like annotate_variation.pl -out output -build ref_version input.vcf  referencedb/) will generate this information. You need not give specific information to generate information about amino acid changes. Annovar will automatically produces two files: output.variant_function and output.exonic_variant_function. The second file contains amino acid changes as a result of the exonic variant as shown below (taken from Annovar website, http://annovar.openbioinformatics.org/en/latest/user-guide/gene/).

line9 nonsynonymous SNV IL23R:NM_144701:exon9:c.G1142A:p.R381Q, 1 67705958 67705958 G A comments: rs11209026 (R381Q)

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by Ashutosh Pandey11k

This is not my question, I already have this data, that is simply the amino acid change. I am speaking about the actual codon change. For example if it changes from the R to Q amino acid, I have heard that ANNOVAR can return the specific codon for R and then the specific codon for Q. This is what I am trying to obtain. I already am retrieving the results that you mention above. 

ADD REPLYlink written 3.8 years ago by dahliashvets10
1

My bad. Well I looked into the output files from Annovar and I am afraid that it doesn't give you the "before" and "after" codon information. I guess the easiest way would be to rerun annotation for your vcf file using snpEff which writes the information you are looking for in the output file. See below:

G	A	100.0	PASS	AF=0.0005;EFF=STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q236*|749|NOC2L||CODING|NM_015658|)
ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by Ashutosh Pandey11k

Okay sounds good, thank you so much for looking into it! I just wanted to know if there did exist a way to do this in Annovar before I looked at other options. 

Thanks again!!!

ADD REPLYlink written 3.8 years ago by dahliashvets10
1

<plug>VEP also does this in its default output</plug>

:-)

ADD REPLYlink written 3.8 years ago by EnsemblWill560

Thanks so much for the tip!

ADD REPLYlink written 3.8 years ago by dahliashvets10
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