# Option B: From BSSH
Use this option when you already have sequencing data (FASTQ, BAM, or CRAM files) and want to generate the noise baseline from existing files.
## Step-by-Step Instructions
1. **If starting from BCL files:** First run BCL Convert (from Run Planner or the BCL Convert app) to generate FASTQ files.
2. Open the **Baseline Builder** application in BaseSpace Sequence Hub (BSSH) or the systematic noise file app on Illumina Connected Analytics (ICA).
3. Complete the analysis name and select where to save your results.
4. Select **Systematic noise** in the application settings.
5. Select your input reads (FASTQ, BAM, CRAM, or ORA files).
6. Pick **hg38 v6** and **hg19 v6** with or without pangenome.
7. Enable the **IDT Custom panel** checkbox.
8. Upload your target BED file.
9. In **SNV Systematic noise VCF type**, choose **gVCF with BP\_RESOLUTION**.
10. The set **Noise Threshold for VC Excluded regions** is set to **0.02**.
11. **Samples per node** defaults to 5 but can be adjusted based on your throughput needs.
12. Launch the analysis.
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