Question: Annovar Annotate VCF tool - empty tabular file
gravatar for Kostas
3.3 years ago by
Kostas10 wrote:

Hello everyone,

I am using a regular vcf file as input for the ANNOVAR Annotate VCF tool. Note that I use Galaxy public server. Using "edit attributes" I set hg19Patch10 as reference genome of the vcf file.

ANNOVAR accepts the input file but as output it returns an empty tabular file with the message:


format: tabular, database: hg19Patch10

Log: tool progress Log: tool progress NOTICE: Finished reading 783 lines from VCF file NOTICE: A total of 725 locus in VCF file passed QC threshold, representing 625 SNPs (443 transitions and 182 transversions) and 121 indels/substitutions NOTICE: Finish

Why am I getting an empty tabular file?

Do I need to install ANNOVAR or use Tool Shed with a cloud or local Galaxy (as mentioned in this post: ) in order to get the results? And does this include the option to use mouse reference genome for different vcf files?

I must also note that I am using a vcf file with only one sample.



vcf annovar • 1.7k views
ADD COMMENTlink modified 2.2 years ago by marcocassone0 • written 3.3 years ago by Kostas10
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The database "hg19" is the genome indexed for this tool on Please rerun this way and the problems will likely resolve.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.3 years ago by Jennifer Hillman Jackson25k

Hello Jennifer, I've had the same problem and I've tried what you said,using hg19 database, but didn't work. It still empty and they say:

Log: tool progress Log: tool progress Unknown option: vcfinput Usage: [arguments] <query-file> <database-location>

 Optional arguments:
        -h, --help                      print help message
        -m, --man
ADD REPLYlink written 2.6 years ago by yasminlima0

Hello, Annovar is working as far as I can tell from testing at Perhaps double check your inputs (specifically, the chromosome identifiers in your VCF dataset versus those in hg19 from UCSC) and give the tool another test run using the latest version. It could be that there is no overlap between the input VCF and the datasets selected, but that is a content issue you will need to confirm, it is not a code/usage issue.

If there are still problems after confirming these items, please submit a shared history link along with a link to this post to and we can review. Thanks, Jen

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Jennifer Hillman Jackson25k
gravatar for marcocassone
2.2 years ago by
marcocassone0 wrote:

i have the same problem... please help me

ADD COMMENTlink written 2.2 years ago by marcocassone0
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