auto_annovar

[abakelaar]

can anyone tell me what's wrong


[abakelaar@iPipeline annovar]$ perl auto_annovar.pl -model recessive 0004_61WDG_s_5 humandb/hg18/ --buildver hg18 NOTICE: the --ver1000g argument is set as '1000g' by default

NOTICE: Running step 1 with system command <annotate_variation.pl -geneanno -buildver hg18 -dbtype refgene -outfile 0004_61WDG_s_5.step1 0004_61WDG_s_5 humandb/hg18/>
Can't exec "annotate_variation.pl": No such file or directory at auto_annovar.pl line 131.
Error running system command: <annotate_variation.pl -geneanno -buildver hg18 -dbtype refgene -outfile 0004_61WDG_s_5.step1 0004_61WDG_s_5 humandb/hg18/>

[scd]

Annovar requires that the annotate_variation.pl script is somewhere in your global execution path.

What I've done is make a symbolic link in /usr/local/bin that points to the annotate_variation.pl script.

Use ln -s to do so (http://unixhelp.ed.ac.uk/CGI/man-cgi?ln)

[tmacme]

Hey guy,
When I finished making the "symbolic link" as you indicated , the "Error running system command" message was still there ,with the message "Can't exec "annotate_variation.pl" missed. And now I was so confused.
[ps] I use Cygwin.