Biostar Beta. Not for public use.
Question: Genome Browser and Custom Tracks
0
Entering edit mode

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 3.0 years ago justinms • 10
Entering edit mode
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 3.0 years ago
Eric Lim
♦ 1.4k
Entering edit mode
0

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

ADD REPLYlink 3.0 years ago
justinms
• 10
Entering edit mode
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 3.0 years ago
Eric Lim
♦ 1.4k

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.0