Expected normal ploidy buffer filter

The Expected normal ploidy buffer filter can be added to filter chains in the software to detect mosaic chromosomal aneuploidies in research samples and to set a buffer for normal ploidy values (2 for autosomes, 2 for X chromosomes in females, and 1 for X and Y chromosomes in males) so as to identify the most likely aneuploidy samples. Ploidy calls do not have to be integers because mosaicism detection allows decimal-level Copy Number Gain or Loss calls.

By default, the filter is set to filter out all copy number variant segments of gain or loss within 0.2 ploidy value of expected normal. Gains must be above ploidy 2.2 and below ploidy 1.8 to remain filtered in on autosome and female X, and ploidy 1.2 and ploidy 0.8 on male Y. Filter conditions include the ability to change the amount of buffer by adjusting the From and To values. This Expected Normal Ploidy Buffer overrides any Confidence filtering that may be in effect within the buffer zone.

If default settings are applied, ploidy values of 1.8 to 2.2 are filtered out as normal for autosomes and X chromosomes in females, and 0.8 to 1.2 are filtered out as normal for X and Y chromosomes in males. Values outside this range are detected as chromosomal ploidy samples.