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. For navigating to your results in the BSSH or ICA UI, see Where to Find Your Results.