Steps in analysis workflow creation

Research Application

Use this analysis workflow step to select a research application and a sample group to use in a custom analysis workflow.

The research application and sample group settings affect the options that are available in subsequent analysis workflow creation steps. This step applies to all analysis workflow types.

If you copy an existing analysis workflow, you cannot change its research application.

Reference

Use this analysis workflow step to select a reference genome type and to upload the appropriate reference files that the analysis will use to focus the analysis in the custom analysis workflow.

The predefined analysis workflows that use a human reference are designed to work with the hg19 human reference genome.

Custom Ion AmpliSeq™ DNA panels can be designed to work with the GRCh38 human reference genome.

For more information about uploading panel files, see Import panel files from AmpliSeq.com

Primers

Use this analysis workflow step to select the primers used in the library preparation in a metagenomics custom analysis workflow.

For more information, see Create a custom analysis workflow for use with Metagenomics research application and Custom primer sequences for Metagenomics analysis workflows.

Annotation

Use this analysis workflow step to select annotation sets that are specific for the custom analysis workflow.

Annotation sets contain various annotation sources that provide information about the biological meaning of variants and allow variant sorting and prioritization.

Many annotation sources are available in this step that are derived from public and private annotation databases for hg19 and GRCh38. If the annotation set that you need is not available for selection, you can create a new annotation set from the Workflow Presets screen. For more information, see Create annotation set workflow presets.

Filters

Use this analysis workflow step to establish a default filter chain to use for the custom analysis workflow. All future analyses that are run through this analysis workflow will use this filter chain.

Filter chains are sets of filters that you apply to variants identified in your analysis. Filters allow you to remove or include variants in your analysis results. For more information, see Filters and filter chains.

Copy Number

Use this analysis workflow step to select a copy number baseline to apply to the custom analysis workflow. The copy number baseline identifies the copy number variants (CNVs) in samples.

This analysis workflow step applies only to DNA, aneuploidy, and some Oncomine™ analysis workflows.

Analysis workflows that use copy number baseline controls can provide better copy number detection than paired sample analysis workflows.

Copy number baseline choices are limited to copy number baselines that were created using the hotspots and target regions file that is selected in the Reference step of the workflow bar.

For more information, see Apply a copy number baseline workflow preset to an analysis workflow

Fusion

Use this analysis workflow step to select a baseline that provides a reference point against which fusion calls that are based on an expression imbalance are made with the RNA Exon Tiling assays that are included in a panel.

If the panel contains at least one RNAExonTile target, you must select an RNA baseline that corresponds to the panel content.

Plugins

Use this analysis workflow step to apply available plugins to a custom analysis workflow. Plugins provide additional functionality and content to an analysis workflow. Applying a plugin is optional.

This analysis workflow step applies only to DNA, DNA and fusions, fusions, annotate, and aneuploidy analysis workflows.

The Oncomine™ Variant Annotator plugin is selected by default for some Oncomine™ analysis workflows and all Ion AmpliSeq™ HD analysis workflows.

Analysis workflows for Oncomine™ assays and analysis workflow templates for Ion AmpliSeq™ HD panels in Ion Reporter™ Software include the Oncomine™ Variant Annotator plugin. The plugin integrates into analysis results data from more than 24,000 exomes across solid tumor and hematological cancer types, and annotates variants relevant to cancer with Oncomine™ Gene class and Oncomine™ Variant class information. For more information and a full list of annotation rules for each Oncomine™ assay, see Oncomine Variant Annotator plugin criteria, or contact your local support representative, Field Bioinformatics Specialist (FBS), or Clinical Account Consultant (CAC).

Use the Oncomine™ Variant Annotator plugin with Oncomine™ panels only.

Final Report

Use this analysis workflow step to specify the final report template that will report the variants used in the analysis in the custom analysis workflow.

If a final report template is not available, you can set up a new template. Final report templates are available for selection in this step. If the final report template that you need is not available for selection, you can create a new final report template from the Workflow Presets screen. For more information, see Create a final report template workflow preset.

Parameters

Use this step to review or modify runtime parameters to refine and optimize the custom analysis workflow. Many fixed and community panels imported from AmpliSeq.com include optimized variant calling parameters.

Parameter categories include: annotation, bamstats, CNV finding, MSI, read mapping, and variant finding. All analysis workflow types allow some parameter custom settings. The parameters that you can customize vary by analysis workflow.

For more information, see Customize tuning parameters

Confirm

This analysis workflow step is the final step that you must complete to create custom analysis workflow. All analysis workflows include this step.