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ClawBio
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claw-methylation-cycle

Analyzes methylation cycle enzyme activity and BH4 capacity from raw SNP genotype files.

1.1k|257|Updated Feb 25, 2026
Search Tags:#bioinformatics#genomics#genotype#methylation#snp analysis#mthfr#bh4
One-click install
npx skills add https://github.com/ClawBio/ClawBio --skill claw-methylation-cycle
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: claw-methylation-cycle
Source: https://github.com/ClawBio/ClawBio/tree/main/skills/claw-methylation-cycle
Command: npx skills add https://github.com/ClawBio/ClawBio --skill claw-methylation-cycle

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Interpreting raw consumer genotype data (23andMe, AncestryDNA, ADNTRO) for methylation cycle variants like MTHFR C677T/A1298C requires manual lookup of each SNP and literature-based activity estimates. This Skill automates that analysis, producing enzymatic activity profiles, a Net Methylation Capacity score, BH4 axis estimates, and compound heterozygosity detection for clinician review.

Core Features & Use Cases

  • 9-Gene Methylation Panel: Scores MTHFR, MTRR, MTR, CBS, BHMT, SHMT1, COMT, and AHCY variants with literature-cited activity percentages.
  • Composite Scores: Computes Net Methylation Capacity (NMC) and BH4 axis capacity with dopamine/serotonin synthesis impact estimates, plus MTHFR compound heterozygosity detection.
  • Clinician-Reviewed Output: Generates a Markdown report and structured result.json with prioritized, citation-backed genotype findings and RUO disclaimers.
  • Use Case: A clinician receives a patient's 23andMe raw data file and asks about MTHFR status; the Skill parses the file, flags compound heterozygosity, and outputs a report with literature-referenced findings for clinical contextualization.

Quick Start

Run the methylation cycle analysis on my raw genotype file and generate the clinical report and JSON output in a results folder.

Frequently Asked Questions about claw-methylation-cycle

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I analyze MTHFR variants from a 23andMe raw data file?▼

Run the methylation_cycle.py script with --input pointing to your 23andMe raw genotype file and --output for the results directory. It parses rsID-genotype mappings, scores MTHFR C677T and A1298C, and writes a report.md plus result.json with activity estimates.

What genotype file formats does this methylation analysis support?▼

It accepts tab-delimited raw SNP files in 23andMe, AncestryDNA, or ADNTRO format with rsid, chromosome, position, and genotype columns. VCF, FASTQ, BAM, and PLINK binary files are not supported and require preprocessing first.

What is the Net Methylation Capacity score?▼

NMC is a weighted composite index (0-100) of estimated enzyme activities, with MTHFR weighted at 0.35 as the rate-limiting enzyme. Scores below 40 indicate severely reduced capacity; missing SNPs are excluded and reported via a coverage percentage.

Can this tool diagnose methylation disorders or recommend supplement doses?▼

No. It is a research-use-only genotype reporting tool, not a diagnostic device. It flags findings like MTHFR compound heterozygosity for qualified clinician review and never provides dosing, diagnosis, or direct patient instructions.

What happens if my genotype file is missing some panel SNPs?▼

Missing SNPs are marked as not assessed and excluded from the NMC calculation rather than assumed normal. The output reports snps_missing and a coverage percentage so partial scores are interpreted with caution.

Does this skill cover pharmacogenomics like CYP enzymes or warfarin risk?▼

No. Pharmacogenomic questions involving CYP enzymes, SLCO1B1, statins, or anticoagulation are out of scope and belong to the PharmGx Reporter skill. This skill covers only the 9-gene methylation cycle panel.

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