> For the complete documentation index, see [llms.txt](https://help.bioinsight.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.bioinsight.illumina.com/dragen-somatic-for-idt-custom-panels/stage-2-run-variant-calling/variant-calling.md).

# Inputs and Modes

After generating your systematic noise file, you can run the DRAGEN for IDT Custom Panels variant calling pipeline. The pipeline is pre-optimized for IDT xGen cfDNA and FFPE library chemistry, so you do not need to adjust calling parameters manually.

## Required Inputs

* Sample reads: FASTQ, BAM, CRAM, or ORA files
* Systematic noise file (from [Stage 1](/dragen-somatic-for-idt-custom-panels/stage-1-generate-systematic-noise-file/noise-baseline.md))
* Target panel BED file
* *(Optional)* Block-zone BED file for additional filtering

## Choose Your Launch Path

* [Option A: Launch from Run Planner](/dragen-somatic-for-idt-custom-panels/stage-2-run-variant-calling/option-a-run-planner.md) — for new sequencing runs (tumor-only).
* [Option B: Launch from BSSH or Platform Core](/dragen-somatic-for-idt-custom-panels/stage-2-run-variant-calling/option-b-bssh-ica.md) — for existing data or tumor-normal analysis.

## Sample Type Considerations

If you are working with formalin-fixed paraffin-embedded (FFPE) samples that show significant DNA degradation, see [Low-Quality FFPE Mode](/dragen-somatic-for-idt-custom-panels/stage-2-run-variant-calling/ffpe-mode.md) before launching.


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