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hammerlab / cycledash

Variant Caller Analysis Dashboard and Data Management System
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VCF comparison table showing incorrect results #822

Closed jaclynperrone closed 9 years ago

jaclynperrone commented 9 years ago

I tried a couple comparisons on http://cycledash.demeter.hpc.mssm.edu/ and the table is showing incorrect values for True Positives compare1

ihodes commented 9 years ago

Could you link the run this is seen on?

On Mon, Aug 31, 2015 at 12:46 PM, Jaclyn Perrone notifications@github.com wrote:

I tried a couple comparisons on http://cycledash.demeter.hpc.mssm.edu/ and the table is showing incorrect values for True Positives and False Negatives.

[image: compare1] https://cloud.githubusercontent.com/assets/5685044/9584266/3bc2fa6a-4fde-11e5-8904-f83f322a9289.png

— Reply to this email directly or view it on GitHub https://github.com/hammerlab/cycledash/issues/822.

jaclynperrone commented 9 years ago

Surely! http://cycledash.demeter.hpc.mssm.edu/runs/267/examine?query=ORDER+BY+contig%2C+position

ihodes commented 9 years ago

False negatives tentatively look correct (the false negatives are variants which are found in the VCF being compared to, but not in the variants you're examining). True positives bear some looking into.