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Genomic Coordinates Converter

Converts and checks genomic coordinates and variants so bioinformatics joins don't silently go wrong

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
10 files

What it does

When a bioinformatics analysis moves positions between file formats, genome builds, or tools, a one-base shift or mismatched assembly can produce plausible but wrong results with no error. This skill teaches the agent the coordinate conventions (0-based half-open vs 1-based inclusive), provides scripts to convert intervals, normalise and compare variant representations against a reference FASTA, and check whether files use compatible assembly and contig names. The agent uses these tools to verify positions rather than converting from memory.

Great for

  • Bioinformaticians merging BED, GTF, VCF or SAM files from different sources
  • Researchers suspecting an off-by-one or wrong genome build in their results
  • Analysts comparing indels from different callers or databases such as ClinVar

Skip it if

  • General-purpose coding or non-genomic data tasks, where the skill is not relevant
  • Clinical decisions on patient variants without validated pipelines and expert review, since the scripts are diagnostic helpers and not production VCF rewriters (use bcftools norm for production work)

Try asking

  • “My BED peaks don't overlap my GTF genes, could it be a 0-based vs 1-based problem?”
  • “Convert chr7:5530601-5530625 from UCSC format to BED”
  • “Check whether these two variant files were both built on GRCh38 before joining them”
  • “Are chr1:7:CAC:C and chr1:2:GCA:G the same deletion? Normalise both against my reference”
Step-by-step guide: how to use Genomic Coordinates ConverterInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 10 original files, the MIT licence and an attribution note.

    genomic-coordinates.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip genomic-coordinates.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip genomic-coordinates.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • Provide the reference FASTA and its .fai index so variant normalisation can check REF alleles and avoid loading the whole genome into memory.
  • Use check_contigs.py before any join to catch chr-prefix or build mismatches early.
  • For production VCF rewriting, use bcftools norm; this skill's TSV output discards genotypes and annotations.

What's inside

  • references/format-conventions.md
  • references/reference-builds.md
  • references/transcript-coordinates.md
  • references/variant-representation.md
  • scripts/_common.py
  • scripts/audit_intervals.py
  • scripts/check_contigs.py
  • scripts/convert_coords.py
  • scripts/normalize_variant.py
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.