Create an Expected Normal Ploidy Buffer filter chain

Mosaic analysis workflows can increase the frequency of false positives around normal ploidy, which is 2N for autosomes and the X chromosome in females, or 1N for sex chromosomes in males. You can create an Expected Normal Ploidy Buffer (ENPB) filter chain and add it to an analysis workflow to filter false positives in these analyses.

When you create the filter chain, you can adjust the range values when to customize the amount of buffer. For more information about the filter, see Expected normal ploidy buffer filter.

IMPORTANT! If using a single filter with a NOT operator, do not use a parenthesis. If parenthesis is used, the filter chain can be saved but an error occurs when applying the filter chain in analyses results. For example, use NOT Filtered Coverage instead of NOT (Filtered Coverage).

  1. In the Workflows tab, click Presets.
  2. Click Create Preset > Filter Chain.
  3. In the Create Filter Chain dialog box, select the dropdown list of filter chains, and enter Expected to find, then select the Expected Normal Ploidy Buffer filter chain.
  4. Set the filter chain values and settings.

    Option

    Description

    Expected Normal Ploidy Buffer filter

    By default, the ENPB filter filters out all copy number variant segments of gain or loss within 0.2 ploidy value of expected normal. With this setting, you can set the filter to filter ploidy changes for the following ranges:

    • between 2.2 and 1.8 on autosomes and female X chromosomes

    • between 1.2 and 0.8 on male X and Y chromosomes

    Confidence

    A log ratio that is between the called ploidy state likelihood of the region and the expected ploidy state likelihood.

    Large confidence values increase the likelihood that the software results indicate that the ploidy state differs from what is expected.

    Recommended values: > .1 for non-mosaic ploidy calling and for high-sensitivity detection, and > 1 for mosaic ploidy calling.

  5. Enter a name and, optionally, a description.
  6. Click Save.

The ENPB filter chain can now be added to a mosaic analysis workflow. When an analysis is launched with the analysis workflow, the ENPB filter chain filters for false positives. For more information, see Add a filter chain to an analysis workflow, Create a custom analysis workflow for mosaicism, No Gender, or different tile sizes, and Launch an analysis.