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  • ANNOVAR quick start up guide

    Hello, I am very new to Bioinformatics and coding, so any help is appreciated.

    I have run into an issue early one using the quick start up guide.

    In the first box of executable code, I have no problem downloading the different databases. However when I try actually running the last line:

    ----------------------

    $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

    -----------------------

    I run into the following error message:

    ---------------------

    Running with system command <perl C:\Users\orp\OneDrive - UW\Documents/annotate_variation.pl -geneanno -buildver hg19 -dbtype refGene -outfile myanno.refGene -exonsort -nofirstcodondel example/ex1.avinput humandb/>
    Can't open perl script "C:\Users\orp\OneDrive": Permission denied
    Error running system command: <perl C:\Users\orp\OneDrive - UW\Documents/annotate_variation.pl -geneanno -buildver hg19 -dbtype refGene -outfile myanno.refGene -exonsort -nofirstcodondel example/ex1.avinput humandb/>

    ----------------------

    I am thinking this might be related to something about not having proper admin level access on the computer (I am using my computer at work, where I have needed admin access to download/install any software)?

    Thanks for your help. It's very appreciated.

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