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Genomic Coordinates

Prevents silent off-by-one and wrong-build errors whenever genomic coordinates cross a file format, tool, or assembly boundary.

Data & AnalyticsIntermediate★ 33,030⑂ 3,248AI score 9/10Last updated: Aug 9, 2026

What it does

  • Coordinate conversion: rule-table based conversion between 0-based half-open (BED, bedGraph, PSL, genePred) and 1-based inclusive (GFF/GTF, VCF, SAM, WIG, Picard interval_list) via convert_coords.py, including region strings like chr7:5,530,601-5,530,625.
  • Variant normalisation: normalize_variant.py trims to parsimony and left-aligns indels against a reference FASTA, compares whether two records describe the same change, and enforces splitting multi-allelic records with --split before normalising. Every REF is verified against the FASTA.
  • Assembly and contig checks: check_contigs.py reads .fai, .chrom.sizes, VCF/SAM headers, FASTA, BED and GTF to identify GRCh37 vs hg19 vs GRCh38 vs T2T, chr-prefix mismatches, length conflicts, and coordinates past contig ends.
  • File auditing: audit_intervals.py surfaces evidence of coordinate mistakes (start_below_one, many_zero_length, past_contig_end, not_parsimonious, bad_alt_allele) and exits 1 on fatal findings, so it works as a CI gate.
  • Transcript/CDS/protein positions: clarifies HGVS c. numbering, GFF phase, minus-strand direction, and points you to VEP, bcftools csq, Mutalyzer or the hgvs package instead of hand arithmetic.

Who it's for

  • Bioinformaticians and pipeline engineers working with WGS/WES data
  • Clinical genomics teams joining or deduplicating variants against ClinVar/gnomAD
  • Anyone who has been burned by mixing outputs from bedtools, samtools, bcftools, UCSC and Ensembl

Example uses

  1. "Convert peaks.bed to GTF coordinates" → start +1 only, with zero-length features flagged as unrepresentable.
  2. "My indels don't match ClinVar" → split multi-allelics, left-align normalise, then --compare two representations for equivalence.
  3. "Joining variants.vcf with annotation.gtf gives odd results" → run check_contigs.py to detect GRCh37/hg19/GRCh38 mixing and chr-prefix mismatch.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/genomic-coordinates/SKILL.md

What I want: (describe your task here)

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↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/genomic-coordinates folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/genomic-coordinates/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git && mkdir -p ~/.claude/skills && cp -r scientific-agent-skills/skills/genomic-coordinates ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and clone the repo: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git
  2. Make sure the skills folder exists: mkdir -p ~/.claude/skills
  3. Copy just this skill: cp -r scientific-agent-skills/skills/genomic-coordinates ~/.claude/skills/
  4. Check your Python version: python3 --version (3.11+ required; no third-party packages needed).
  5. For variant normalisation, have a reference FASTA ready, ideally with a .fai index (samtools faidx ref.fa).
  6. Restart Claude Code and try a prompt like "convert this BED file to VCF coordinates" or "normalize this indel against GRCh38" to trigger the skill.
View source on GitHub ↗License: MIT