`finaletoolkit frag-length-intervals`¶

1. About¶

Retrieves fragment length summary statistics over intervals defined in a BED file.

Where frag-length-bins gives one distribution for the whole genome, this gives summary statistics per genomic window: the mean, median, standard deviation, minimum and maximum fragment length in each interval. This turns fragment length from a single sample-level profile into a spatial signal, so regions where cfDNA is systematically shorter or longer than the genome average can be located.

In this pipeline the intervals are the fixed-size windows tiling the genome, built at the start of each run at the width given by --interval (default 1mb).

2. As the pipeline runs it¶

finaletoolkit frag-length-intervals bams/{sample}.sorted.bam <intervals> \
    -q <--mapscore> \
    -min <--fragment-minimum> \
    -max <--fragment-maximum> \
    -p any \
    -o frag_length_intervals/{sample}_frag_interval.bed \
    -w <threads> \
    -v

2.1 Arguments¶

input_file

The analysis BAM. value: bams/{sample}.sorted.bam

interval_file

Windows to summarize over. value: intervals/{genome}_{size}_intervals.bed, tiled from the selected --genome build's reference FastA at the --interval width

See Reference files.

-q, --quality-threshold

Minimum mapping quality. value: --mapscore (default 20)

-min, --min-length / -max, --max-length

Fragment length window. value: --fragment-minimum / --fragment-maximum (defaults 50 / 500)

Note that this truncates the distribution before the statistics are computed, so the reported mean and standard deviation describe fragments inside the window only.

-p, --intersect-policy

How a fragment is assigned to an interval. value: any

A fragment contributes to every window it overlaps. A long fragment spanning a window boundary is therefore counted in both, which is the right behavior for characterizing the fragment population present at a locus. Double counting at boundaries matters more the narrower the --interval width is.

-w, --workers

Worker processes. value: the step's threads from config/cluster.json (default 16)

Short-read threshold is left at its default

FinaleToolkit accepts -s, --short-reads to set the threshold defining the short-read fraction (default 150 bp). The pipeline does not override it. If you need short-to-long fragment ratios as a feature, delfi computes them explicitly and with GC correction.

3. Output¶

frag_length_intervals/{sample}_frag_interval.bed — a BED where each interval carries its fragment-length summary statistics: mean, median, standard deviation, minimum and maximum.

4. Controlling it¶

What	How
Whether this step runs	requires a non-zero `--split-interval`
Fragment length window	`--fragment-minimum`, `--fragment-maximum`
Which windows	`--interval`, which sets the width the windows are tiled at
Threads / memory / walltime	the `frag_length_intervals` entry of `config/cluster.json`

"frag_length_intervals": {
    "threads": 16,
    "mem": "8G",
    "time": "08:00:00",
    "partition": "norm"
}

5. Requires¶

A non-zero --split-interval (default 5000), and reference_fa for the selected build, which the interval BED is tiled from. Both bundled builds provide it.

finaletoolkit frag-length-intervals¶