Secondary Pipelines

Secondary pipelines take raw sequencer output and produce called variants. They are the expensive, CPU-and-storage-intensive step in the workflow — typically tens of minutes to hours per sample depending on coverage and panel size.

Inputs

• FASTQ — paired-end reads, gzipped.
• BAM (alternative starting point) — aligned reads, optionally pre-deduplicated.

Outputs

• VCF — variants called against the reference genome, normalised.
• BAM — aligned, sorted, deduplicated reads (input to downstream visual review).
• QC metrics — coverage, contamination, sample-swap checks.

Available workflows

• Somatic workflows — tumor-only and tumor–normal pipelines for cancer analysis.
• Germline workflows — single-sample and trio pipelines for hereditary analysis.

See also

• Tertiary pipelines — consume the VCF produced here.
• Running an analysis — UI flow.