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.