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

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.

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ADD REPLYlink written 16 months ago by Eric Lim550

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

ADD REPLYlink written 16 months ago by justinms0

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 16 months ago by Eric Lim550
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