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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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Bedpe Output #219

Closed mej54 closed 6 years ago

mej54 commented 6 years ago

Hi Ryan,

I'm running Lumpy with the bedpe output option, and am wondering what the score represents in column 8? Is that the quality score of the variant, or does it have something to do with the probability of the reported breakpoints within the predicted interval?

lumpybedpe
ryanlayer commented 6 years ago

You can just ignore that score. It is a measure of the probability distribution width vs height. We hoped that it would help us identify high- vs low-quality SVs, but it never really worked.

On Mon, Dec 4, 2017 at 12:27 PM, Molly Johnson notifications@github.com wrote:

Hi Ryan,

I'm running Lumpy with the bedpe output option, and am wondering what the score represents in column 8? Is that the quality score of the variant, or does it have something to do with the probability of the reported breakpoints within the predicted interval? [image: lumpybedpe] https://user-images.githubusercontent.com/10553651/33571742-fe098e8a-d8fe-11e7-97e2-4659fa0925f0.png

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/arq5x/lumpy-sv/issues/219, or mute the thread https://github.com/notifications/unsubscribe-auth/AAlDUUV26QsxWy9waDiUBpjKCydbRFRJks5s9EekgaJpZM4Q1Lq5 .

-- Ryan Layer

mej54 commented 6 years ago

Good to know, thanks!