Question: Having trouble running ANNOVAR annotator for the first time please help!
0
gravatar for screadore
7 days ago by
screadore0
screadore0 wrote:

Hey guys so I'm trying to run ANNOVAR for the first time on a Windows x64 Dell laptop. The following issues have occured:

H:\>perl C:\Users\SCreadore\Desktop\annovar\table_annovar.pl example/ex1.avinput humandb/ -buildver hg19 -out myanno -remove -protocol refGene,cytoBand,dbnsfp30a -operation g,r,f -nastring . -csvout -polish -xreffile example/gene_fullxref.txt

Output: Error: the required database file humandb\hg19_refGene.txt does not exist.

I used the following commands on the ANNOVAR website to set it up and it still gives me the error above:

perl C:\Users\SCreadore\Desktop\annovar\annotate_variation.pl -buildver hg19 -downdb -webfrom annovar refGene humandb/

perl C:\Users\SCreadore\Desktop\annovar\annotate_variation.pl -buildver hg19 -downdb cytoBand humandb/

perl C:\Users\SCreadore\Desktop\annovar\annotate_variation.pl -buildver hg19 -downdb -webfrom annovar exac03 humandb/ 

perl C:\Users\SCreadore\Desktop\annovar\annotate_variation.pl -buildver hg19 -downdb -webfrom annovar avsnp147 humandb/

perl C:\Users\SCreadore\Desktop\annovar\annotate_variation.pl -buildver hg19 -downdb -webfrom annovar dbnsfp30a humandb/

perl C:\Users\SCreadore\Desktop\annovar\table_annovar.pl example/ex1.avinput humandb/ -buildver hg19 -out myanno -remove -protocol refGene,cytoBand,exac03,avsnp147,dbnsfp30a -operation gx,r,f,f,f -nastring . -csvout -polish -xref example/gene_xref.txt

So I'm not exactly sure of what the issue is. So any advice or help would be greatly appreciated.

software error • 49 views
ADD COMMENTlink written 7 days ago by screadore0

Be wary of the directory dividers \ /, which are different across Windows and Mac / Linux. If you look in the humandb directory, can you find file there?

Did this return any output?

perl C:\Users\SCreadore\Desktop\annovar\annotate_variation.pl -buildver hg19 -downdb -webfrom annovar refGene humandb/
ADD REPLYlink modified 6 days ago • written 6 days ago by Kevin Blighe61k

Check if the file "hg19_refGene.txt" exists or not. if yes, you can specify the path of the file manually.

ADD REPLYlink written 5 days ago by thind.amarinder20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1684 users visited in the last hour