annovar output problems

[Bioinforquestion]

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?

Thanks.

[marco12345]

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

[Heisman]

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.

[marco12345]

Hi,

I have trouble making Annovar’s gene annotation tool work well.

I am working on a virus, so had to build the reference by myself following Annovar’s website indications. I so build the refGene file, the refLink one, and through Annovar’s retrieve_seq_from_fasta.pl, the fasta file. I then run a vcf file, already passed through the convert2annovar.pl script in order to prepare it correctly for the input, and had as a result every variant listed as “intergenic”.

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

File samples (I’ll 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.
ATGGATCTGCAAAGACATCCGATTCCGTTTGCGTGGCTAGATCGAGACAAAGTTGAGCGTCTTACAGATTTTCTCAGCAATTTGGAAAGACTGGATAATGTAGATTTGCGAGAGCATCCCCATGTGACTAA....

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.