Is GATK germlineCNVcaller's QS metric deletion size dependent?
I just wanted to check an intuition I got from looking at my gCNV output graphically. Most of the very large deletions (>1Mbps) the caller has detected in my data have a QS of 3077 (which appears to be some upper bound), but I also have the occasional very large deletion with QS 100-150, which is above the suggested cutoff for deletions QS>100, but seems comparatively very very low.
Is it safe to assume that QS is size dependent and therefore a QS in the range of 100-200 might not be adequate evidence of a deletion for a deletion of size >1Mbps in the way it could be for a much smaller deletion?
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