CLI Reference

./cigar-sashimi [wrapper-options] --bam <BAM> --region <CHR:START-END> [core-options]

The cigar-sashimi wrapper consumes the output/rendering options below itself and forwards everything else to the analysis core. For svg/html output it runs the core and the renderer as a pipeline; for json it runs the core alone.

Wrapper options

Option	Default	Description
-f, --format <type>	svg	svg, html, or json.
-o, --output <path>	cigar-sashimi.<fmt>	Output path. JSON goes to stdout when omitted.
--width <px>	1200	Figure width (svg/html only).
--height <px>	860	Figure height (svg/html only).
--intron-scale <r>	0.05	Intron compression ratio, 0–1 (svg/html only).
--show-novel-exon	off	Highlight assembly exons absent from the reference GTF.
--include-first-last-exon	off	Also highlight terminal exons (excluded by default).
--show-novel-intron	off	Highlight assembly introns absent from the reference GTF.
--merge-insertion-sources	off	Merge nearby coverage-track and assembly insertions with similar sequence into one gap.
-h, --help		Show wrapper help.

For svg/html output the wrapper also writes the intermediate JSON next to your file (plot.svg → plot.json).

Analysis options (core)

All of the following are forwarded to cigar-sashimi-core.

Input

Option	Default	Description
-b, --bam <FILE>	required	Indexed BAM file.
-r, --region <REGION>	required	chr:start-end, 1-based inclusive.

Filtering

Option	Default	Description
--min-mapq <INT>	10	Skip reads below this mapping quality.
--exclude-flags <INT>	0x904	Drop reads matching any of these SAM flag bits (decimal or 0x hex). The default excludes secondary, supplementary, and unmapped reads.
--min-junction <INT>	2	Minimum supporting reads for a junction arc.
--junc-cov-ratio <FLOAT>	0.01	Minimum junction count relative to flanking coverage.
--min-deletion <INT>	2	Minimum supporting reads for a deletion arc.
--min-del-len <INT>	1	Minimum deletion length (bp).
--min-insertion <INT>	2	Minimum supporting reads for an insertion cluster.
--min-ins-len <INT>	5	Minimum insertion length to consider (bp).
--min-softclip <INT>	2	Minimum supporting reads for a soft-clip cluster.
--min-clip-len <INT>	20	Minimum soft-clip length to consider (bp).
--ins-cov-ratio <FLOAT>	0.05	Minimum insertion/soft-clip count relative to local coverage.

Clustering

Insertions and soft clips are grouped by sequence similarity using minimizers. These control that grouping; the defaults rarely need changing.

Option	Default	Description
-k, --kmer-size <INT>	15	Minimizer k-mer size.
-w, --window-size <INT>	10	Minimizer window size.
--min-jaccard <FLOAT>	0.6	Minimum Jaccard similarity to place two events in the same cluster.

Annotation & intron compression

Option	Default	Description
--gtf <FILE>	—	Reference GTF for the gene model. Overrides coverage-based exon/intron detection.
--assembly <FILE>	—	Assembly GTF (e.g. assembled insertion/soft-clip transcripts) drawn as a second track.
--intron-cov <FLOAT>	10.0	Coverage-based detection: max average depth for a window to be called intron (used only when no --gtf is given).
--intron-window <INT>	25	Coverage-based detection: window size in bp.
--no-compression	off	Disable exon/intron detection and intron compression entirely.

Renderer (direct use)

The renderer can be run on its own against core JSON:

node render/src/cli.js --input data.json --format html --output plot.html

Option	Default	Description
--input <path>	- (stdin)	Input JSON, or - for stdin.
--format <type>	svg	svg or html.
--output <path>	- (stdout)	Output path, or - for stdout.
--width <px>	1200	Figure width.
--height <px>	860	Figure height.
--intron-scale <f>	0.05	Intron compression ratio, 0–1.
--merge-insertion-sources	off	Merge nearby coverage-track and assembly insertions.
--show-novel-exon	off	Highlight novel assembly exons.
--include-first-last-exon	off	Include terminal exons in novel highlighting.
--show-novel-intron	off	Highlight novel assembly introns.

Filtering thresholds are applied by the core, not the renderer.

Examples

Interactive HTML over a gene with a reference annotation:

./cigar-sashimi \
  --bam sample.bam \
  --region chr7:55019017-55211628 \
  --gtf gencode.gtf \
  --format html \
  --output egfr.html

Inspect raw JSON:

./cigar-sashimi --bam sample.bam --region chr7:55019017-55211628 --format json