Custom analysis workflows for aneuploidy research

To create a new analysis workflow for use with Ion ReproSeq™ aneuploidy research, you can copy and edit a predefined analysis workflow.

You can enable mosaicism detection, a software setting that allows non-integer ploidy calls and reports a CNV event as a decimal ploidy value instead of an integer value. For each tile that is shown in analysis results, the algorithm fits the data to all ploidy with a step of 0.05. You can further customize mosaicism detection with the Expected Normal Ploidy Buffer (ENPB) filter. For more information, see Predefined filters and Create an Expected Normal Ploidy Buffer filter chain.

You can also improve the detection of small segmental CNV events in Ion ReproSeq™ analysis workflows for use with aneuploidy research. The CNV Transition Penalty parameter establishes the trade-off between false-positive and false-negative rates. The transition penalty is a probability that the copy-number state changes for any given random tile. For more information, see Improve detection of small segmental CNV events.

IMPORTANT! Do not change parameters from the default settings unless you understand how the change can affect your analysis.