This filter can be added to filter chains in the software to make ploidy estimates with lower and upper confidence values on somatic samples. The filter detects extra copies over the expected normal ploidy value (2 for autosomes, 2 for X chromosomes in females, and 1 for X chromosomes in males). The 5% lower confidence bound value is the ploidy estimate where there is a 5% chance that the true ploidy is below that value. The 95% upper confidence bound is the ploidy estimate where it is 95% certain that the true ploidy is below that value. The lower bound is the most important for gains. The upper bound is most important for losses.
By default, the filter is set to detect gains and losses using the confidence interval values of 5% confidence interval for Minimum Ploidy Gain over the expected value and 95% confidence interval for Minimum Ploidy Loss under the expected value. The default boundary values are set to 0.0.
Gene A—A gene with suspected gain of 5% CI = 4.1 and 95% CI = 10.3 filtered in.
Gene B—A gene with suspected loss of 5% CI = 0 and 95% CI = 1.0 filtered in.
Gene C—A gene with suspected gain of 5% CI = 2.2 and 95% CI = 3.6 filtered out (2.2 is less than 4).
Gene D—A gene with suspected gain of 5% CI = 2.1 and 95% CI = 5.2 filtered out (2.1 is less than 4).
Gene E—A gene with 5% CI = 0.8 and 95% CI = 2.1 filtered out (0.8 is less than 4 and 2.1 is greater than 2).