Analysis outputs and figures

Analysis outputs are requested with their own flags, with or without construct files.

Analysis reports

Tables of ranked candidates, predicted epitopes and applicable manufacturability metrics.

Flag	Output
--output-ascii-report	Plain-text summary
--output-html-report	HTML report
--output-pdf-report	PDF report (wkhtmltopdf or WeasyPrint backend)
--output-xlsx-report	Excel workbook with one sheet per variant
--output-csv	Flat CSV
--output-json-file	Full ranked-vaccine-peptides graph as JSON

Neoepitope report

A per-(peptide, allele) table in XLSX or CSV, chosen by file extension. It is the default output of the LENS / pVACseq input path and is also available on the full pipeline.

Flag	Output
--output-neoepitope-report	XLSX (default) or CSV (by extension)

Mutation and assembly figures

vaxrank-mutation-figure turns the Isovar table produced by --output-isovar-csv into publication-ready, white-background transcript and protein context figures. When the input includes the optional *_cdna_sequence and *_cdna_variant_{start,end} columns, each variant also gets a 5-prime-to-3-prime nucleotide comparison. Both views separate the reference transcript, the annotation-only mutant prediction and the RNA-assembled sequence, so unsupported or assembly-refined claims stay explicit.

The random predictor below is for testing the figure workflow only.

vaxrank --vcf variants.vcf --bam tumor-rna.bam \
  --mhc-predictor random --mhc-alleles 'HLA-A*02:01' \
  --output-isovar-csv patient-isovar.csv

vaxrank-mutation-figure patient-isovar.csv \
  --output-root figures \
  --variant DYNC1H1 \
  --format svg --format pdf --format png \
  --png-scale 3

Outputs are grouped under figures/YYYY-MM-DDTHHMMSSZ/. Every variant gets an SVG, a PDF, a high-resolution PNG (3600×2100 at the default 3× scale) and a compact JSON record. The figure and JSON distinguish annotation gene/transcript provenance from RNA-assembly provenance. The run manifest records the input checksum, Vaxrank version, formats, raster dimensions and file inventory. Omit --variant to render every row. Use --timestamp for reproducible builds or tests; an existing run is never overwritten.

Evidence figures for structural variants

For structural variants and fusion junctions, use a cross-platform evidence JSON rather than an Isovar table:

vaxrank-evidence-figure evidence.json \
  --output-root evidence-figures \
  --format svg --format pdf --format png

This view keeps DNA, short-read RNA, short-read assembly and long-read RNA as separate evidence stages. It displays the junction nucleotide sequence and withholds a protein unless the input supplies an established coding sequence. See examples/osteosarc_evidence_figures/ for DNA-only, cross-platform, matched-sample long-read rescue, and unresolved long-read-only examples.

Complex-result figures

To show the downstream Vaxrank decision rather than the evidence alone, use a complex-result record. This view separates DNA interpretation, RNA support, translated protein, target epitopes and the final vaccine-construct selection:

vaxrank-complex-result-figure results.json \
  --output-root result-figures \
  --combined-output vaxrank-complex-variant-results.pdf

The timestamped run contains a compact combined PDF and one high-resolution PNG/SVG page per result. See examples/osteosarc_complex_results/ for a real assembly-dependent frameshift selection, an assembled indel with no passing binder, an ambiguous fusion held out of ranking, and an unresolved long-read fusion whose protein is deliberately withheld.