exporting raw data from CNV Summary track in Broad IGV
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9.4 years ago
sic ▴ 10

Hi,

I'm looking at ~1000 genomes in IGV, at the CNV summary track. Looks like the summary bins are 200kb, and when you mouse over them the track gives you a summary of # genomes where the region is amplified vs deleted. Which is nice visually, but I'd like to get the raw data exported, not just a picture of the track.

Now clearly I could go through the data and build the bins/calculate the frequencies myself, but since IGV is clearly doing it already, I'm wondering if anyone knows a way to save the raw summary track data. This is my first time using IGV, I've googled around a bit, but apologies if it's something very obvious I'm not seeing.

chr13 cnv summary

TCGA IGV Broad CNV • 3.6k views
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