> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/dragen-somatic-for-idt-custom-panels/workflow/workflow.md).

# Workflow Overview

The DRAGEN for IDT Custom Panels workflow is a verified workflow that supports the flexibility needed for custom panels while delivering reproducible results with minimal parameter tuning. The workflow has **three entry points** to meet customers where they are.

The DRAGEN for IDT Custom Panels workflow enables a verified workflow that complies with the flexibility needed for custom panels but delivers reproducible results with minimal parameter tunning required.

## Two-Stage Analysis

Regardless of which entry point you choose, the analysis consists of two stages that must be run in order:

1. **Stage 1: Generate a systematic noise baseline file.** See [Stage 1: Generate Systematic Noise File](/dragen-somatic-for-idt-custom-panels/stage-1-generate-systematic-noise-file/noise-baseline.md).

<figure><img src="/files/mjDmcv6QY5gBfpxEODr3" alt=""><figcaption></figcaption></figure>

1. **Stage 2: DRAGEN somatic for IDT custom panels variant calling.** See [Stage 2: Run Variant Calling](/dragen-somatic-for-idt-custom-panels/stage-2-run-variant-calling/variant-calling.md).

<figure><img src="/files/5EvqJbwmiCfqrHqLNxla" alt=""><figcaption></figcaption></figure>

{% hint style="info" %}
**NOTE.** The output VCF can be ingested into [Illumina Connected Insights](/dragen-somatic-for-idt-custom-panels/qc-and-interpretation/connected-insights.md) for tertiary analysis interpretation.
{% endhint %}

## Next Step

Use [Choose Your Entry Point](/dragen-somatic-for-idt-custom-panels/workflow/entry-points.md) to decide whether to launch from Run Planner, the BSSH application, or the ICA pipeline.


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