[BioC] Complete variant toolbox: gmapR/VariantTools/VariantAnnotation

Julian Gehring julian.gehring at embl.de
Sun Dec 8 19:13:59 CET 2013

Hi Thomas,

In this case, I assume that you are referring to columns added by 
functions of the 'VariantTools' and 'gmapR' packages.  These are simply 
additional columns in a 'VRanges' object and not part of a standard 
'VRanges' class.  'help("tallyVariants", package = "VariantTools")' goes 
a bit into the details.

Best wishes

On 12/08/2013 06:54 PM, Thomas Girke wrote:
> Hi Julian,
> Yes, I have seen it, but I cannot find explanations for things like
> "n.read.pos", "mean.quality.ref", etc. In most cases I can guess what
> it is but often I am not sure.

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