ANNOVAR ability to report reference and mutant codon

Question

[dahliashvets]

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!

[Ashutosh Pandey]

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

[dahliashvets]

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

[Ashutosh Pandey]

The default command (something 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)

[dahliashvets]

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.

[Ashutosh Pandey]

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|)

[dahliashvets]

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!

[EnsemblWill]

<plug>[VEP][1] also does this in its default output</plug>

:-)

[dahliashvets]

Thanks so much for the tip!