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Updated Oct 19, 2026

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Audit genomic intervals before downstream analysis

genomic-interval-audit is an offline coordinate and format audit for BED, GTF, GFF3 and VCF files.

Agent
Locate reversed intervalsCheck reference boundsReview coordinate heuristics

overview

What genomic-interval-audit does

Audit a BED, GTF, GFF3 or VCF file against its own coordinate conventions (off-by-one evidence, end before start, zero-length features, contigs or positions outside a genome) with K-Dense's genomic-coordinates audit. JSON findings; offline.

Return JSON findings with severity, rule, line or file location and detail. Checks include impossible coordinates, end-before-start records and suspicious zero-length BED patterns. An optional genome-size file adds unknown-contig and reference-bound checks.

Supply a relative input path inside the source folder, up to 512 MiB. Optional format selects bed, gtf, gff3 or vcf. Fatal findings remain successful report data; path, format or usage errors fail the job. A clean report has an empty findings list. Inputs are unchanged.

Packaged version: 065b734. Upstream license: MIT.

source github.com/k-dense-ai/scientific-agent-skills/tree/065b734670d7d990627dbc06a05b5a99be33f1f1/skills/genomic-coordinates

use cases

Where genomic-interval-audit fits

Locate reversed intervals

Receive line-level findings when an end precedes its start.

Check reference bounds

Supply genome sizes to detect unknown contigs and out-of-range coordinates.

Review coordinate heuristics

Investigate suspicious zero-length patterns before joining interval files.

reference

genomic-interval-audit inputs and flags

4 inputs
NameTypeFlagDescription
sourceFOLDER--sourceFolder holding the interval/variant file and an optional genome sizes or .fai file.
fileSTRING--filePath of the BED/GTF/GFF3/VCF file inside the folder (maximum 512 MiB).
genomeSTRING--genomeOptional path of a chrom.sizes or .fai file inside the folder, for contig and bounds checks.
formatSTRING--formatOptional format override (bed, gtf, gff3, vcf); detected from the extension otherwise.

Showing key inputs. genomic-interval-audit exposes 4 inputs in total.

example

Run genomic-interval-audit

genomic-interval-audit · command
python3 /app/run.py --source ./source --file peaks.bed --genome genome.sizes ./output

guidance

Choosing genomic-interval-audit

Use genomic-interval-audit to find suspicious coordinates before interval arithmetic. It does not repair records or prove that a clean file uses the intended coordinate convention. Contig compatibility across multiple files is a separate check.

faq

genomic-interval-audit questions

source: Folder holding the interval/variant file and an optional genome sizes or .fai file. file: Path of the BED/GTF/GFF3/VCF file inside the folder (maximum 512 MiB). genome: Optional path of a chrom.sizes or .fai file inside the folder, for contig and bounds checks. format: Optional format override (bed, gtf, gff3, vcf); detected from the extension otherwise.

Return JSON findings with severity, rule, line or file location and detail. Checks include impossible coordinates, end-before-start records and suspicious zero-length BED patterns. An optional genome-size file adds unknown-contig and reference-bound checks.

Supply a relative input path inside the source folder, up to 512 MiB. Optional format selects bed, gtf, gff3 or vcf. Fatal findings remain successful report data; path, format or usage errors fail the job. A clean report has an empty findings list. Inputs are unchanged.

Use genomic-interval-audit to find suspicious coordinates before interval arithmetic. It does not repair records or prove that a clean file uses the intended coordinate convention. Contig compatibility across multiple files is a separate check.

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.

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Run genomic-interval-audit yourself

The saved verifier confirmed end_before_start on line 3, contig_not_in_genome on line 4 and the file-level many_zero_length warning. These are verifier-confirmed findings, not a retained complete report. The command shows the container entrypoint with example paths.

Open genomic-interval-audit in the libraryBuild a workflow with it

Facts on this page come from the live Trickest tool library.