Annovar Annotate VCF tool - empty tabular file

Question: Annovar Annotate VCF tool - empty tabular file

3.3 years ago by

Kostas • 10

Greece

Kostas • 10 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:

empty

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: https://biostar.usegalaxy.org/p/8508/ ) 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

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modified 2.2 years ago by marcocassone • 0 • written 3.3 years ago by Kostas • 10

3.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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

Thanks, Jen, Galaxy team

ADD COMMENT • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k

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: table_annovar.pl [arguments] <query-file> <database-location>

 Optional arguments:
        -h, --help                      print help message
        -m, --man

ADD REPLY • link written 2.6 years ago by yasminlima • 0

Hello, Annovar is working as far as I can tell from testing at http://usegalaxy.org. 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 galaxy-bugs@lists.galaxyproject.org and we can review. Thanks, Jen

ADD REPLY • link modified 2.6 years ago • written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

2.2 years ago by

marcocassone • 0

marcocassone • 0 wrote:

i have the same problem... please help me

ADD COMMENT • link written 2.2 years ago by marcocassone • 0

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