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VQSR outcome plot

Hi there,

The VQSR outcome plot contrasts filtered versus retained calls. Looking through the code, it appears that calls with LOD<0 are labelled filtered and others retained.

However as I understand it, the actual ApplyRecalibration step simply relies on LOD rankings, not a specific LOD threshold. Do I have that right?

So, are the filtered/retained points in the outcome plot really filtered and retained respectively?

Also, is there a special meaning to 0 as a cutoff point for LOD?

Thanks very much!

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