CLI Reference

Krewlyzer provides a command-line interface for all feature extraction tools.

Main Command

krewlyzer run-all -i sample.bam --reference hg19.fa --output results/

See run-all for the unified command that runs all features.

Command	Description
`extract`	Extract fragments from BAM
`fsc`	Fragment Size Coverage
`fsd`	Fragment Size Distribution
`fsr`	Fragment Size Ratio
`wps`	Windowed Protection Score
`motif`	End Motif extraction
`ocf`	Orientation-aware Fragmentation
`region-entropy`	TFBS/ATAC entropy
`region-mds`	Per-gene MDS
`mfsd`	Mutant Fragment Size Distribution
`uxm`	Fragment-level Methylation
`build-pon`	Build Panel of Normals