bio-variant-normalization
Normalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from different callers or preparing VCF for downstream analysis.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-normalization --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: bcftools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Variant Normalization Left-align indels and split multiallelic sites using bcftools norm. ## Why Normalize? The same variant can be represented multiple ways: ``` # Same deletion, different representations chr1 100 ATCG A (right-aligned) chr1 100 ATC A (left-aligned, normalized) chr1 101 TCG T (different position) ``` Normalization ensures consistent representation for: - Comparing variants from different callers - Database lookups (dbSNP, ClinVar) - Merging VCF files ## bcftools norm **Goal:** Left-align indels and check reference allele consistency. **Approach:** Use bcftools norm with a reference FASTA to shift indels to the leftmost position and optionally fix/exclude REF mismatches. **"Normalize my VCF before comparing callers"
- Version Compatibility
- Why Normalize?
- bcftools norm
- Left-Align Indels
- Check for Normalization Issues
- Multiallelic Sites
- Split Multiallelic to Biallelic
- Split SNPs Only
- Split Indels Only
- Join Biallelic to Multiallelic
- Split Options
- Combined Normalization
- Standard Normalization Pipeline
- Remove Duplicates After Splitting
bcftools norm -f reference.fa input.vcf.gz -Oz -o normalized.vcf.gz bcftools norm -f reference.fa -c s input.vcf.gz > /dev/null Reports REF allele mismatches bcftools norm -m-any input.vcf.gz -Oz -o split.vcf.gz bcftools norm -m-snps input.vcf.gz -Oz -o split_snps.vcf.gz bcftools norm -m-indels input.vcf.gz -Oz -o split_indels.vcf.gz bcftools norm -m+any input.vcf.gz -Oz -o merged.vcf.gz bcftools norm -f reference.fa -m-any input.vcf.gz -Oz -o normalized.vcf.gz bcftools index normalized.vcf.gz bcftools norm -f reference.fa -m-any -d exact input.vcf.gz -Oz -o normalized.vcf.gz
What does the bio-variant-normalization skill do?
Normalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from different callers or preparing VCF for downstream analysis.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-normalization --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.