Fragment Size Distribution (FSD)
Command: krewlyzer fsd
Purpose
Computes high-resolution (5bp bins) fragment length distributions per chromosome arm.
Biological Context
cfDNA fragmentation patterns at chromosome arms can reflect nucleosome positioning, chromatin accessibility, and cancer-specific fragmentation signatures. See DELFI method for details.
Usage
krewlyzer fsd sample.bed.gz --arms-file krewlyzer/data/ChormosomeArms/hg19_arms.bed --output output_dir/ [options]
Output
{sample}.FSD.tsv: Frequency of fragment lengths per chromosome arm.
Options
--arms-file,-a: Chromosome arms BED (required)--threads,-t: Number of processes
Clinical Interpretation
Healthy vs Cancer
| Metric | Healthy Plasma | Cancer (ctDNA present) |
|---|---|---|
| Modal peak | ~166bp | Left-shifted (~145bp) |
| 10bp periodicity | Clear nucleosome signal | May be altered |
| Arm-level variation | Minimal | Increased (correlates with CNAs) |
What to Look For
- Left-shift in distribution: Tumor DNA is typically shorter
- Arm-specific changes: May correlate with copy number alterations
- Loss of nucleosome periodicity: Indicates altered chromatin structure
Reference: See Citation & Scientific Background for detailed paper summary.