ANNOVAR annotate cuts short the VCF file ?

Question: ANNOVAR annotate cuts short the VCF file ?

3.8 years ago by

BC357 • 70

United States

BC357 • 70 wrote:

I uploaded a standard VCF that contains 57651 lines (or 57471 lines variant data) and ran it with ANNOVAR , under usegalaxy.org, to annotate the variants. To my surprise, the output from ANNOVAR contains only 24072 variants. When I aligned the two tables, it's clear ANNOVAR "removed" some of the variants (both novel and known SNPs, granted ANNOVAR on Galaxy only uses snp137) in the original VCF.

Is there some default setting in ANNOVAR that makes some cutoff for variant annotation ? I don't see how I can change any parameter when running ANNOVAR on usegalaxy. Any explanation for the short list of ourput or any suggestion what I could do to re-annotate the VCF? Great many thanks.

annovar • 2.1k views

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modified 3.8 years ago • written 3.8 years ago by BC357 • 70

3.8 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Does the .vcf dataset contain data from multiple samples? If so, this could be the reason for the problem. Do you see this in the info comments of the output?

WARNING to old ANNOVAR users: this program no longer does line-to-line conversion for multi-sample VCF files. If you want to include all variants in output, use '-format vcf4old' instead.

Our team is reviewing the tool wrapper for an update. No ticket has been created yet, but I can provide more feedback next week, if this is your case (please confirm yes/no).

I am assuming that you are using the tool on the public Main Galaxy instance at http://usegalaxy.org. If not, can you reproduce the error on Main? We may ask for you to share the history from Main for troubleshooting if this is not the issue and it is reproducible there (privately, not here in Biostars).

Thanks, Jen, Galaxy team

ADD COMMENT • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

comment cancelled and re-posted as an answer.

ADD REPLY • link modified 3.8 years ago • written 3.8 years ago by BC357 • 70

I am having the same problem. Is there a solution to the problem yet?

ADD REPLY • link written 3.4 years ago by hadaarjan • 0

3.8 years ago by

BC357 • 70

United States

BC357 • 70 wrote:

Sorry for missing your feedback. Indeed, I was using the tool on the public Main Galaxy and did notice the warning of ANNOVAR no longer does line-to-line conversion. From your response, it sounds like the team is reviewing an update to address the issue of ANNOVAR. If correct, is there any fix/solution to this issue of ANNOVAR not doing "line-by-line annotation" during the interim? Thank you.

ADD COMMENT • link modified 3.8 years ago • written 3.8 years ago by BC357 • 70

Hello,

You could split the vcf file by sample, which would be the easiest thing to do. You can always merge again after.

The other option is to update the tool wrapper itself. This would need testing, etc. The comments from the binary are for command-line execution.

I made a ticket for the upgrade request. There is no time-line yet. https://trello.com/c/9puPsRdq

Best, Jen, Galaxy team

ADD REPLY • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k

I split the vcf file by sample and used it as input for ANNOVAR. It worked fine. No warnings. How do I merge the output files for each sample from ANNOVAR?

ADD REPLY • link written 3.4 years ago by hadaarjan • 0

To merge VCF datasets, see the tool "VCFcombine".

To merge BAM/SAM, Bedgraph, and other formats (tabular, interval, bed, gtf), perform a tool search using the keyword "merge".

Best, Jen, Galaxy team

ADD REPLY • link written 3.4 years ago by Jennifer Hillman Jackson ♦ 25k

ANNOVAR gives me tabular data. So I have three tabular data that I need to merge. Is there a right tool on Galaxy main for merging 3 tabular data?

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