Forum: Please Try Out Our Functional VCF Annotation Tool Jannovar
3
gravatar for Manuel
4.8 years ago by
Manuel370
Germany
Manuel370 wrote:

Dear all,

We are looking for testers for updates in our VCF annotation tool Jannovar that was published in [1]. Jannovar offers functional annotation, similar to Annovar and we put a lot of work in keeping its good speed, improving its flexibility, and preciseness in the prediction of protein changes.

If you are looking for an alternative to Annovar or VEP then Jannovar might be useful for you and we would like to ask for you to test our updated version on your data and give us feedback.

You can find binary builds of the latest version (0.11) on GitHub here: https://github.com/charite/jannovar

Synopsis after downloading and extracting:

# java -jar jannovar-cli-0.11.jar download hg19/refseq
# java -jar jannovar-cli-0.11.jar annotate data/hg19_refseq.ser examples/small.vcf
# ls
[...] small.jv.vcf [...]

We are now looking for users who want to try the software on their VCF files and report any problems they stumble over (failure of functional annotation yields [ERROR] lines in the output which we can then use for fixing the problems). We also welcome all other feedback, feature requests and bug reports.

Thanks,
Manuel

[1] Jäger, Marten, et al. "Jannovar: A Java Library for Exome Annotation.Human mutation 35.5 (2014): 548-555.

Edit: Changed the wording.

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Manuel370
1

IMHO instead of asking specifically to break the tool you should simply put out a call that you will assist people in working with the tool  while extolling the great features your tool has. When you call for "break" or "testing" you are basically calling out  people to work for you. When you say we are going to assist you are basically offering to work for others. It is just human nature of better responding to the latter. 

In addition the best tests are those that come from exercising the tool in normal use rather than those devised for features that might break.

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by Istvan Albert ♦♦ 81k

Thank you for your thoughtful comment, I rephrased the entry.

ADD REPLYlink written 4.8 years ago by Manuel370

"If you are looking for an alternative to Annovar or VEP then ...."

I'm not. Why would I be? Is there some deficiency in those tools that you solve? I was happy with Annovar until some downstream tool requested VEP as input. The results are substantially the same.  

Is there any reason to switch again?

ADD REPLYlink written 4.8 years ago by karl.stamm3.5k

Does this work on non-model organisms?

ADD REPLYlink written 4.8 years ago by Adrian Pelin2.3k

If you provide your transcripts in GFF+FASTA, GTF+FASTA or in the UCSC file formats then you can build a Jannovar transcript database and annotate your VCF files, yes. Some of the information required for this can be found here.

What exactly do you want to do? I would be glad to help you writing a datasource definition file and converting the data if necessary. Send me a private message and we will work something out.

ADD REPLYlink written 4.8 years ago by Manuel370

I just realized Biostars does not have a PM function, you can find my email in the Jannovar source code: http://git.io/Hv9bug

ADD REPLYlink written 4.8 years ago by Manuel370

Alright, Thanks! I will give it a try.

ADD REPLYlink written 4.8 years ago by Adrian Pelin2.3k

Note that the definition files should support the file:// pseudo-protocol so you do not have setup a web server with your data. Do not hesitate to send me an email if you run into any problem

ADD REPLYlink written 4.8 years ago by Manuel370
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