Options for generation of publication quality gene diagrams with annotation

Question

[LauferVA]

I want to visualize the variants I have in my VCF (or any tab delimited) file.

Specifically, I want to look at them in relation to annotation tracks such as Cons Score, Encode TFBS binding site, exon or no (and if so what amino acid) and many more.

This can be done through UCSC: https://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=389193029_56wIWP5VNLUDfDyneR3PpEQOJdyN&hgt.psOutput=on

possibly through IGV? And probably through many other tools.

I am writing to ask the community which tools make the best-quality and most attractive graphs for visualizing NGS data?

I would be looking at something between a few hundred bases up to a whole gene (100s to 100000s of bases) so I do not need something like Circos.

Suggestions? Thank you.

Answer 1

[Devon Ryan]

In addition to Gviz, as mentioned by dariober, there's also ggbio. I find both packages pretty useful.

Answer 2

[dariober]

Have a look at the Bioconductor package Gviz and its vignettes for some really pretty graphs. Not sure if it supports VCF, but I'd guess yes. (Obviously assuming you are ok with R)