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problem to download 1000genome database using ANNOVAR

I'm trying to annotate my VCF file using ANNOVAR function table_annovar.pl. There are few files that I need to download before I can use the function. I managed to download all the required files except for 1000 genomes database. Below is the command that I used.

annotate_variation.pl -buildver hg19 -downdb -webfrom annovar 1000g2014oct humandb/

However, I'm getting this error

NOTICE: Web-based checking to see whether ANNOVAR new version is available ... Done
NOTICE: Downloading annotation database http://www.openbioinformatics.org/annovar/download/hg19_1000g2014oct.zip... Done
NOTICE: Uncompressing downloaded files
hg19_1000g2014oct.zip
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.
note: hg19_1000g2014oct.zip may be a plain executable, not an archive
unzip: cannot find zipfile directory in one of hg19_1000g2014oct.zip or
hg19_1000g2014oct.zip.zip, and cannot find hg19_1000g2014oct.zip.ZIP, period.
NOTICE: Finished downloading annotation files for hg19 build version, with files saved at the '1000g' directory

I'm running my analysis on UNIX

annovar
• 4,248 views • link
updated by Ram Ram • written by jan jan

1 answer

Try this:

perl annotate_variation.pl -downdb -webfrom annovar --buildver hg19 1000g2014oct /humandb

Maybe the file is corrupted. Try download again. If error persist then check your administrator to see what is happen with your system.

• 0 views • link
updated by Ram Ram • written by dsmarcoantonio • dsmarcoantonio

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