BRASSVis

Visualize gene fusions and structural variants detected by BRASS (BReakpoint AnalySiS) from whole-genome sequencing data. Based on the Arriba visualization approach adapted for WGS structural variant BEDPE output.

Each fusion is rendered as a multi-panel page showing:

• Chromosome ideograms with breakpoint positions
• Exon structure with intron squishing
• Circos plot for genomic context
• Retained protein domains in the fusion transcript
• Supporting read counts and assembly scores

Installation

# From GitHub
pak::pak("bczech/BRASSVis")

# Or with remotes
remotes::install_github("bczech/BRASSVis")

Dependencies

BRASSVis requires Bioconductor packages GenomicRanges, IRanges, and S4Vectors. These are installed automatically by pak. If installing manually:

BiocManager::install(c("GenomicRanges", "IRanges", "S4Vectors"))

Quick start

From R

library(BRASSVis)

# Generate a full PDF report
brass_report(
  bedpe_path = "results.bedpe",
  gtf_path = "Homo_sapiens.GRCh38.gtf.gz",
  output_pdf = "fusions_report.pdf"
)

With protein domains and custom cytobands

brass_report(
  bedpe_path = "results.bedpe",
  gtf_path = "Homo_sapiens.GRCh37.75.gtf.gz",
  output_pdf = "report.pdf",
  cytobands_path = system.file("ref", "cytobands_hg19_hs37d5_GRCh37_v2.1.0.tsv",
                               package = "BRASSVis"),
  protein_domains_path = system.file("ref", "protein_domains_hg19_hs37d5_GRCh37_v2.1.0.gff3",
                                     package = "BRASSVis")
)

Step by step

# Read BEDPE
fusions <- read_brass("results.bedpe")

# Load annotations
ann <- load_annotations(
  gtf_path = "Homo_sapiens.GRCh38.gtf.gz",
  protein_domains_path = system.file("ref",
    "protein_domains_hg38_GRCh38_v2.1.0.gff3", package = "BRASSVis")
)

# Plot a single fusion
pdf("single_fusion.pdf", width = 11.7, height = 8.3)
plot_fusion(fusions[1, ], fusions, 1, ann$exons, ann$cytobands,
            ann$protein_domains)
dev.off()

From the command line (legacy CLI)

Rscript inst/scripts/BRASSVis.R \
  -i results.bedpe \
  -e Homo_sapiens.GRCh38.gtf.gz \
  -o report.pdf \
  --proteinDomainsFile ref/protein_domains_hg38.gff3 \
  --cytobandsFile ref/cytobands_hg38.tsv

With Docker

docker build -t brassvis .
docker run brassvis Rscript -e 'BRASSVis::brass_report(
  "input.bedpe", "annotation.gtf", "output.pdf")'

Built-in reference data

The package includes cytobands and protein domain annotations for:

Genome	Cytobands	Protein domains
Human GRCh38 (hg38)	Yes	Yes
Human GRCh37 (hg19)	Yes	Yes
Mouse GRCm38 (mm10)	Yes	Yes

Access with system.file("ref", "<filename>", package = "BRASSVis").

Input format

BRASSVis reads annotated BEDPE files produced by BRASS. The file must contain columns: chr1, start1, chr2, start2, strand1, strand2, svclass, gene1, gene2, fusion_flag, and others.

Example output

An example report generated from test data is available in tst/report.pdf.

Exported functions

Function	Description
read_brass()	Parse BRASS BEDPE file
load_annotations()	Load GTF, cytobands, and protein domains
plot_fusion()	Visualize a single fusion event
brass_report()	Generate a complete multi-page PDF report

Authors

• Bartosz Czech
• Pawel Sztromwasser
• Marzena Wojtaszewska

License

GPL-3