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Updated Oct 19, 2026

Bioinformatics

Summarize BED regions with gtars

gtars-stats is an offline BED region statistics node using the gtars CLI.

Agent
Summarize interval sizesInspect chromosome coverage patternsPrepare descriptive QC

overview

What gtars-stats does

Compute native GTARS genomic interval statistics from BED, including region counts, widths, neighbors and chromosome distributions. Uses BED-derived bins, without reference genome annotations.

Validate and normalize the first three tab-separated BED columns, then return native genomicdist JSON with region counts, mean width, widths, neighbors and chromosome distributions. Extra columns are ignored; blank and comment lines are skipped.

Input must contain at least one region with 0 <= start < end <= 2147483647. Limits are 20 MiB, 500000 rows, 120 seconds, one Rayon thread, 2 GiB virtual memory and 50 MiB native output or log. The source file remains unchanged.

Packaged version: 0.10.0. Upstream license: BSD-2-Clause.

source github.com/databio/gtars/tree/90141b683aaa1c5bae4d452718fc440825a5f711

use cases

Where gtars-stats fits

Summarize interval sizes

Receive counts, mean width and the width distribution.

Inspect chromosome coverage patterns

Compare the distribution of supplied regions across contigs.

Prepare descriptive QC

Review region statistics before a separate enrichment or annotation stage.

reference

gtars-stats inputs and flags

1 inputs
NameTypeFlagDescription
inputFILE--inputPlain-text tab-delimited BED file; first three columns used. Nonempty positive-width intervals, max 20 MiB and 500000 rows.

Showing key inputs. gtars-stats exposes 1 inputs in total.

example

Run gtars-stats

gtars-stats · command
python3 /app/run.py --input ./input.txt ./output

guidance

Choosing gtars-stats

Use gtars-stats for descriptive interval statistics. Region bins are derived from the supplied BED and are not fixed reference-genome bins for cross-file comparisons. This node supplies no TSS, GC, genome-partition or enrichment analysis.

faq

gtars-stats questions

input: Plain-text tab-delimited BED file; first three columns used. Nonempty positive-width intervals, max 20 MiB and 500000 rows.

Validate and normalize the first three tab-separated BED columns, then return native genomicdist JSON with region counts, mean width, widths, neighbors and chromosome distributions. Extra columns are ignored; blank and comment lines are skipped.

Input must contain at least one region with 0 <= start < end <= 2147483647. Limits are 20 MiB, 500000 rows, 120 seconds, one Rayon thread, 2 GiB virtual memory and 50 MiB native output or log. The source file remains unchanged.

Use gtars-stats for descriptive interval statistics. Region bins are derived from the supplied BED and are not fixed reference-genome bins for cross-file comparisons. This node supplies no TSS, GC, genome-partition or enrichment analysis.

The public image repository gives immutable image and ORAS download commands, the expected source/notices bundle checksum and pinned upstream source directions. The accompanying OCI bundle retains the original build recipe, runtime sources and full installed notices. The Git recipe keeps primary notices and an exact layer/hash index; it does not duplicate the full installed notice tree or mirror every upstream source archive. Image, source and license notice downloads.

Run gtars-stats yourself

The saved verifier confirmed three regions with widths 10, 20 and 30 and mean width 20 across chr1 and chr2. These are verifier-confirmed values; the complete native JSON was not retained. The command shows the container entrypoint with example paths.

Open gtars-stats in the libraryBuild a workflow with it

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