Creating D4 files

Choose Create D4 and provide:

  • a coordinate-sorted BAM with BAI/CSI, or a CRAM with CRAI;
  • for CRAM, the matching FASTA and .fai index;
  • a new output path ending in .d4.

Use the same reference assembly as the tracks and annotations you plan to compare. Conversion cannot correct an assembly mismatch.

Windows macOS Linux
Create D4 dialog (Windows) Create D4 dialog (macOS) Create D4 dialog (Linux)

The screenshot uses a generated BAM; supply your own indexed alignment file.

Coverage mode

Mode Counts
Standard Aligned bases; CIGAR gaps excluded; overlapping mates counted once.
Fast Whole read spans, including CIGAR gaps; overlapping mates counted twice.
Fragments Proper paired-template spans, including the insert.

Settings

Basic settings selects files and mode. Advanced settings provides:

  • minimum MAPQ;
  • include/exclude SAM flags (by default, unmapped, secondary, QC-failed, and duplicate reads are excluded: 0x704; supplementary reads are not);
  • read groups and absolute template-length limits;
  • BAM/CRAM decompression threads (default: 2).

Choose Create D4 to start. The viewer stays usable during conversion. On completion, choose Add to view to display the result; the file is saved even if you do not add it.

D4 Plot builds secondary-frame and sum indexes, verifies the file, and publishes it without replacing an existing destination. Cancellation or failure before publication removes the temporary result.