Adding Additional Annotations In Annovar

Question

[cable82]

How can I add additional annotations like the gwas db or omim db to the output of summarize_annovar.pl either as an option for that script or after the output is already generated? Either way, I want these databases added to my annotated variant list from the summarize_annovar.pl script.

Also, I need to convert my output file generated from Annovar back into the VCF format. I have not seen anywhere on the Annovar page about doing this, so would I need to manually do it?

Any help would be much appreciated.

Thanks,
Nathan

[aneekbiotech]

Hi Mr. Nathan,

I am facing a similar problem what you have faced in your query 2.6 years ago. Annovar is now upgraded to use table_annovar.pl script instead of summarizeannovar.pl for the same input. I need to add an extra column in the annotated excel output (variant list) with the OMIM ID for each gene. Could you kindly share how you solved this problem or what scripts you have used. It would be a great help for me. I have downloaded the mim2gene.txt file from OMIM but is not sure how to use this file in annovar for annotation. You can send me the details in my email address ([e-mail]) also. Thanks.

[guerrero.kether]

Hi,

Did you solve this problem? because I am stuck at this step. I am trying to use genemap2.txt with the table_annovar.pl I am not a bioinfo, so I do not know what to change in the script.

Thank you

Answer 1

[Sean Davis]

For adding to summarize_annovar output, you would have to modify the actual script or write another postprocessing script that adds the annotations you like.

As for converting to VCF output, I think that is another script that you would need to write.

[cable82]

I figured I would have to write scripts for this...thanks.

Answer 2

[DG]

You may want to look at Variant Tools as an option. You would need to write a format description file for the output of the summarize_annovar.pl script but you can then import and update variants and add additional sources of annotation, including omim and gwas db that Variant Tools supports. Variants are imported into an sqlite3 database, which you can then do selects and manipulations on, as well as output data in various formats including vcf. A bit of a learning curve, and you may need to modify some format description files to get the exact import/output specifications you want, but it is quite useful.

My only major complain with it so far is that it has a tendency to duplicate records. So if you annotate a variant with ccds annotations, and the exon has multiple ccds records (which they usually do) it will duplicate the record instead of merging the ccds IDs together. There is probably a way around this though, I just haven't figured it out yet.

[cable82]

Thanks, I will check this out.