Displaying Genetic Association P-Values In The Ucsc Genome Browser
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9.2 years ago

We would like to display the -log(P-value) for selected GWAS hits as a custom track in the UCSC genome browser. I would like to be able to view these values of the significance test both by genome position and by that -log value so that we can compare physical position and strength of significance, respectively.

At this point, I have built a text file for the few dozen genomic regions of interest and mapped (for viewing) each GWAS SNP solely by location. This was done in the GFF format per UCSC guidelines. Which alternate format should I use in order to display relative values such as the -log(P-value) in a vertical direction? Although GFF supports gray-scale, we find this less visually informative for a single SNP's tick mark than "height" on the y-axis.

ucsc gwas visualization • 2.8k views
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4
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9.2 years ago

The BedGraph format will allow you to visualize these data:

Format Description

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Thank you, Zev. Your recommendation is better than reading the docs on all the format options. I'll try BedGraph.

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