Workflow presets

Workflow presets are the components that are used in creating an analysis workflow. You can create custom workflow presets, then later apply the presets to analysis workflows.

The following lists and describes the types of workflow presets that are available or can be created in Ion Reporter™ Software.

Table 1. Copy Number Variant detection
Workflow preset type	Description
Annotation Sets	A set of annotation sources to use for variants in the Annotation step of creating an analysis workflow. For more information, see Create annotation set workflow presets.
Annotation Source	Annotation sources to use for variants in the Annotation step of creating an analysis workflow. For more information, see Create annotation set workflow presets.
Filter Chains	A set of filters to use for variants in the Filter step of creating an analysis workflow For more information, see Create a user-defined filter chain
Copy Number Baselines	A set of control samples that are used to create a baseline for detecting CNVs in single-sample workflows. The baselines are available in the Copy Number step when you create an analysis workflow. For more information, see Copy Number Variant detection. For more information, see Copy Number Variant detection.
Sequence Variant Baselines	Used in single sample analysis workflows for removing false positive variants that occur due to a sequencing error. For more information, see Sequence variant baselines.
Final Report Templates	Final report templates that are available to use in the Final Report step of creating an analysis workflow. For more information, see Create a final report template workflow preset.
Fusion Panels	The tab-delimited BED file that defines the coordinates of amplicons. Fusion panels are added in the Reference step when you create an analysis workflow that includes fusions.
Target Region Files	Target regions files restrict analysis to only regions specified in the file. These BED files are available to use in the Reference step of creating an analysis workflow. For more information, see Upload a target regions BED file workflow preset.
Hotspot Region Files	Hotspot files cause the hotspot positions to be listed in the analysis results, even if a variant is not called at those positions. These BED files are available to use in the Reference step of creating an analysis workflow. For more information, see Upload a hotspots BED file workflow preset.