Question: Genome Browser and Custom Tracks
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gravatar for justinms
5 months ago by
justinms0
justinms0 wrote:

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?

ADD COMMENTlink written 5 months ago by justinms0
1

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.

enter image description here

ADD REPLYlink written 5 months ago by khericlim330

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

ADD REPLYlink written 5 months ago by justinms0
1

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.

ADD REPLYlink written 5 months ago by khericlim330
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