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The quality score for each base was used as an indicator of base call uncertainty.
This function incorporates copy number call uncertainty by using a latent class model as described in [ 4].
Rare variant collapsing methods are being further developed and extended to account for direction of effect, probability that a variant be functional, and genotype or sequence call uncertainty.
To date, only one other R package, CNVtools[ 5], has been developed that can appropriately incorporate CNV copy number call uncertainty in the test for association between CNVs and disease.
Simulated case-control data was generated for different sample sizes (500 cases and 500 controls; 2,000 cases and 2,000 controls), and different degrees of call uncertainty, from very little uncertainty (Q = 6) to a moderate-high degree of uncertainty (Q = 3).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com