This is my first time using galaxy. I ran Free Bayes to detect the variants of a data set against the reference genome, but can't classify the kinds of variants I got according to it's types(snp,mnp,ins,..).
So i'm asking if there is a tool that can help me detect the number of each variant in my VCF.
Thanks in advance.
See the tools in the group "VCF Manipulation" and "NGS: Variant Analysis". The tool "VCFfixup" may be what you want just to gather counts (from say, Freebayes), but there are many other functions available: compare to reference annotations, etc.
If you use Mileup or Naive Variant Caller instead, there are other tool options. See the tool forms to understand which accept these specific input formats.
Additional tools for use in a local/cloud can also be found in the Tool Shed. Just search by "vcf" to bring up the full list of options. 3rd party documentation will help you to understand what each does.
Best, Jen, Galaxy team