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Old 09-09-2015, 09:15 AM   #1
kostask
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Location: Greece

Join Date: Sep 2015
Posts: 8
Default Annovar no such file or directory

Hi everyone,

I'm new to Annovar so I tried to follow the Quick Start-Up Guide for table_annovar program.

Specifically I downloaded hg19 refGene database (perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar refGene humandb/) and then I used table_annovar.pl for the example data, (table_annovar.pl example/ex1.avinput humandb/ -buildver hg19 -out myanno -remove -protocol refGene -operation g -nastring . -csvout).

Everything worked fine and I got the .csv output file: "Multianno output file is written to myanno.hg19_multianno.csv"

However I cannot open the following output files:

"Output files were written to myanno.refGene.variant_function, myanno.refGene.exonic_variant_function"

and I get back a no such file or directory error.

Any idea what's happening?

I am running Cygwin in Windows 8.1 and I have installed all Perl modules.
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Old 09-10-2015, 01:21 AM   #2
jesus garcia
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Location: madrid

Join Date: Nov 2011
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Hi kostask,

If you use the -remove option (table_annovar.pl example/ex1.avinput humandb/ -buildver hg19 -out myanno -remove -protocol refGene -operation g -nastring . -csvout) the several files that was created to obtain the results will be deleted. This happens with the files you ask for, if you want to conserve these, you need remove this option.

Hope this help you,
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Old 09-11-2015, 03:55 AM   #3
kostask
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Location: Greece

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Thanks jesus garcia, it works fine now!
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