Output Files

Each run creates a timestamped output folder under your -o path.

Files

  • pyfuse_output.xlsx: full annotation table
  • pyfuse_fusion_annotation.html: interactive HTML table with sorting/filter/search
  • pyfuse_output.vcf: BND-style VCF representation
  • pyfuse_fusion_summary.txt: fusion summary counts
  • excluded_breakpoints.txt: entries filtered during preprocessing
  • pyfuse_<timestamp>.log: runtime logs

HTML report behavior

In the HTML report:

  • gene partners are hyperlinked to GeneCards
  • coordinates/transcripts are hyperlinked to UCSC and RefSeq locations
  • DataTables controls support filtering and search
  • fusion plots are linked as separate HTML files by default; use --fusion-plot-mode embed only when you want one self-contained HTML report and the file size is acceptable