Dear all,
I was just wondering, is there a way to visualize variants in a VCF file using Gviz? I had a quick look at the vignette and googled around but could not find anything.
Any help appreciated!
cheers, jo
I don't know of a method on a VCF file but if you have a VCF class object you can just extract/manipulate the rowRanges():
DataTrack(rowRanges(myVCF))
Valerie
That works, yes. However, I didn't want to load the full VCF file. I fetched a VcfFile from AnnotationHub and was looking for a possibility to just load variants in the genomic region that is plotted from the file (on the fly). I've just added such a functionality for FaFiles to Gviz... if possible that would be nice for VcfFiles too.
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Have you looked at ggbio for that sort of thing?
No, I haven't, but I will, thanks!