Genome Browser and Custom Tracks

Question

[justinms]

Bio Guys, Does anyone know how to display variant information on the genome browser that displays variant frequency as one would visualize in a lolliplot or manhattan plot?

[Eric Lim]

I don't know if there's a way to display lolliplot using the genome browser, but do you mean something like this? If so, the Genome Graph is probably what you're looking for. The below example was a copy-and-paste version of allele frequencies for SF3B1 from ExAC to the browser using Genome Graph.

[justinms]

This looks nice actually, how exactly did you extract that information from ExAC?

[Eric Lim]

For the example above, I got all the variants for SF3B1 via the export function from the web application, copied the 3 columns that contain chromosome, position, and allele frequencies, and pasted into Genome Graph. To automate the entire genome, I assume it's very doable by simply transforming the ExAC VCF into a tab-delimited file of 3 columns.