HOW can select variations with MAF <0,01 in a VCF files without use ANNOVAR? I have problem with EXOME analysis when I create a VCF files i can't selection MAF<0,001 because ANNOVAR is a FAKE in Galaxy, what's kind of tool i can use ?
There are tools in the group VCF Manipulation to do all types of VCF filtering at http://usegalaxy.org. Do just do plain text filter, the tools in Filter and Sort: Filter and/or Select can be used, as well as many in Text Manipulation (some of the more customizable tools in this last group require unix utility experience, yet we still think they are useful and include them as a convenience. General sci users can disregard them should they not wish to learn the syntax).
If you want to describe the problems you have been having with Annovar, we'd be glad to help. I can let you know that the tool is indexed for the human genome hg19 (the only human build supported). If it is just that you want an update, the tool author can be contacted through the Tool Shed with enhancement requests. As far as I know, this was just the first pass at wrapping of the tool - user feedback about usage are a good thing.
Best, Jen, Galaxy team