# Output Files

The pipeline generates the following key output files.

## Baseline Builder Outputs (Stage 1)

* **Systematic noise file:** `<output>/systematic-noise/systematic-noise-file/systematic_noise_v2.0_systematic_noise.bed.gz`
* **Excluded regions BED:** `<output>/systematic-noise/systematic-noise-file/blocklist.bed`

## Variant Calling Outputs (Stage 2)

For both tumor and normal samples:

* **Alignment file:** `<output>/<sample_name>/*.bam`
* **Variant call annotated file:** `<output>/<sample_name>/*.hard-filtered.vcf.gz`
* **TMB estimate**
* **Coverage and QC statistics**

The VCF file contains both passing variants (`FILTER="PASS"`) and non-passing variants that did not have sufficient supporting evidence.

For details on the most useful VCF fields, see [Key VCF Fields](/dragen-somatic-for-idt-custom-panels/review-outputs/vcf-fields.md). For navigating to your results in the BSSH or ICA UI, see [Where to Find Your Results](/dragen-somatic-for-idt-custom-panels/review-outputs/find-results.md).


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