Annotating VCF file for Allele Frequency

[qissy-bioinfo]

Hi, I annotated my WGS sample using SnpEff in UseGalaxy. But the annotation result, does not include the allele frequency in the VCF file. I was suggested into using OpenCravat. Is there a guide for me to refer to on how to add the allele frequency information using the annotated VCF file I currently have? Looking forward to any responses for reference. Thanks!

[RachelKarchin]

Are you interested in population allele frequency or the variant allele frequency IVAF)?

[qissy-bioinfo]

Population allele frequency

[RachelKarchin]

You've got alot of choices for population allele frequency databases. OpenCRAVAT has eight of them. Check out our annotator store:
https://run.opencravat.org/submit/nocache/index.html?store

Submit your VCF file to OpenCRAVAT and select the allele frequency databases you want to use to annotate your variants.

[qissy-bioinfo]

Hi I tried using gnomAD but the status of the job updated that there was an error. But, I can't seem to view the error

[RachelKarchin]

sorry to hear it. Might you try first submitting your unannotated VCF that you originally submitted to snpeff? I believe the annotations you got from snpeff will also be available from opencravat. If that works, the issue may be the format of the.snpeff vcf. Also, if you could email the snpeff annotated VCF with us, we will try to reproduce your error and figure out what is going on. Thanks again for trying.OpenCRAVAT
our email is karchinlab@gmail.com

[qissy-bioinfo]

Hi! Thank you so much for all the reply. I managed to run a few of the samples. But after running about 2-3 samples, I can't proceed to upload the next VCF file. Does it have like a resting time or limits per day?

[RachelKarchin]

Great! If you can let us know whether you were able to successfully process the VEP-generated VCF or succeeded only with your oeriginal VCF, that would be great! This would allow us to troubleshoot if there are issues with VEP-generated VCFs specifically,.

Please share details about what you mean about being unable to upload a VCF file? Are you getting an error message? If yes, what does it say? If there is no error message, what are the symptoms of your upload failure?

[qissy-bioinfo]

I succeeded annotating the allele frequency using my original SnpEff annotated VCF. But, after submitting 4 files, I wasn't able to proceed with another sample. After I've uploaded the file and chose all the fields required, when I clicked the annotate button the file didn't load at all

[RachelKarchin]

Sounds like progress. I still don't understand what you mean by the "file didn't load at all". Please send a screenshot of what you see when it appears the file is not loading so we can help you figure out what is going on.

[qissy-bioinfo]

So, everytime I clicked on annotate, the screen would show Uploading Input File (1st picture) for 1 second and then disappear. And looking at the table, no new annotations is recorded (2nd picture)

[RachelKarchin]

Thanks vey much for this. It helps alot. The only limitation we are enforcing right now is a 2GB maximum size on input files. Are any of the files that are failing to upload this large?

[qissy-bioinfo]

No, I checked and all the files are in KB.

[RachelKarchin]

Thanks. We will solve this for you. I will reach out to our engineering team tomorrow.

[qissy-bioinfo]

Thank you so much

[RachelKarchin]

Please try again. The really large job has finished. If your jobs are uploaded now, we will know what the problem was previously.
Thanks for your patience.

[qissy-bioinfo]

Hi, I still can't upload the job

[kmoad]

Hi @qissy-bioinfo, I'm one of the oc engineers. Sorry you're having an issue sending jobs.

I've tried running similar size and count of files as yours through a new account and haven't been able to recreate the issue. I'd like a bit more info if possible.

Do you have issues with a specific vcf file, or can you not submit any new jobs at all from your account?

[qissy-bioinfo]

Hi! Thank you so much for actively trying to help me. So I tried with a few different VCF files. It seems I can't submit any new jobs from my account.