Having trouble running ANNOVAR annotator for the first time please help!
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3.9 years ago
screadore ▴ 20

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 • 1.5k views
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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?

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perl C:\Users\SCreadore\Desktop\annovar\annotate_variation.pl -buildver hg19 -downdb -webfrom annovar refGene humandb/
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Check if the file "hg19_refGene.txt" exists or not. if yes, you can specify the path of the file manually.

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