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Old 12-15-2011, 12:39 AM   #1
gary
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Location: Shanghai

Join Date: Dec 2009
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Default annovar running error

I am trying to use annovar to annotate my exome-seq data.
Here is my commend:
summarize_annovar.pl --ver1000g 1000g2011may --verdbsnp 132 --buildver hg19 snp.annovar ./humandb -outfile output.snp

“--ver1000g”was set to “1000g2011may” because I downloaded it from annovar website:
http://www.openbioinformatics.org/an..._download.html

but I still got an error:
Error: the required database file humandb/hg19_ALL.sites.2010_11.txt does not exist. Please download it via -downdb argument by annotate_variation.pl.

Do I need to also get the “hg19_1000g2010nov_all” version?
Could someone please tell me what I’m doing wrong here?

Thanks a lot!
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Old 12-15-2011, 05:35 AM   #2
Heisman
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Default

I just tried and it works for me. Are you sure you have that database downloaded in the /humandb directory? Does it matter that you have "./humandb" instead of "/humandb"? I also didn't include an "-outfile".
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Old 12-15-2011, 06:25 AM   #3
Heisman
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However, you probably have to change line 213 (or around 213) of the summarize.pl script to reflect the version you are running (ie, in your case you will want it to be:

Code:
open (STEP4, "$outfile.hg19_ALL.sites.2011_05_dropped") or die "Error: cannot read from drop file $outfile.hg19_ALL.sites.2011_05_dropped: $!\n";
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