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Old 06-28-2013, 03:50 AM   #1
Location: barcelona

Join Date: Mar 2013
Posts: 18
Question annovar output problems


I have trouble making Annovarís gene annotation tool work well.

I am working on a virus, so had to build the reference by myself following Annovarís website indications. I so build the refGene file, the refLink one, and through Annovarís, the fasta file. I then run a vcf file, already passed through the script in order to prepare it correctly for the input, and had as a result every variant listed as ďintergenicĒ.

I am working on a Mac OSX 10.6.8, but if needed have access to a new Linux environment.
I tried with both the old version of Annovar and the recently released one (few days ago).

The script has been called like this:

/path/.../ --geneanno --outfile sample --dbtype refGene --buildver NC_XXXXX sample.annovar /path/.../NC_XXXXX/

File samples (Iíll just show one line. Notice that the variant I show is exonic):

refGene.txt file (Reference):

94 U11 gene NC_XXXXX - 18924 21578 18965 21578 1 18924 21578 . U11 gene unk unk 2

refMrna.fa file (Reference):

>U11 gene Comment: this sequence (leftmost exon at NC_XXXXX:18924) is generated by ANNOVAR on Fri Jun 28 12:06:03 2013, based on regions speficied in /Users/Marco/Desktop/NC_XXXXXdb/NC_XXXXX_refGene.txt and sequence files stored at /Users/Marco/Desktop/NC_XXXXXdb.

sample.annovar file (input):

NC_XXXXX 20309 20309 A G hom . 5

sample.variant_function (OUTPUT):

intergenic NONE(dist=NONE),NONE(dist=NONE) NC_XXXXX 20309 20309 A G hom . 5

sample.exonic_variant_function (OUTPUT):

This file was empty.

Thanks in advance for the help. If more info are needed, please do not hesitate asking me.
marco12345 is offline   Reply With Quote
Old 06-28-2013, 07:56 AM   #2
Senior Member
Location: St. Louis

Join Date: Dec 2010
Posts: 535

Maybe someone here can help, but in the past I emailed the author of ANNOVAR and he got back to me quickly with help; so if you can't figure it out maybe email him.
Heisman is offline   Reply With Quote
Old 06-28-2013, 08:04 AM   #3
Location: barcelona

Join Date: Mar 2013
Posts: 18

Yeah, that was my next step, but usually this forum works so well that I prefer to try first here.

Thanks for the suggestion anyway
marco12345 is offline   Reply With Quote
Old 10-22-2015, 04:41 PM   #4
Junior Member
Location: Canada

Join Date: Oct 2015
Posts: 1
Default how to build database in annovar for virus

Dear Marco,

I am also working on virus. How did you build the database.

Can you please guide me in building the database for virus?

Bioinforquestion is offline   Reply With Quote

annovar, bash, output, refgene.txt, snp annotation

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