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variant-normalization

Maintainer FreedomIntelligence · Last updated April 1, 2026

variant-normalization.

OpenClawNanoClawAnalysisReproductionvariant-normalizationopenclaw medical skillsadditional scientific toolsvariant

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/variant-normalization

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Left-align indels and split multiallelic sites using bcftools norm.
  • Comparing variants from different callers.
  • Database lookups (dbSNP, ClinVar).
  • Merging VCF files.
  • chr1 100 ATCG A (right-aligned) chr1 100 ATC A (left-aligned, normalized) chr1 101 TCG T (different position).

Source Doc

Excerpt From SKILL.md

Why Normalize?

The same variant can be represented multiple ways:


## Left-Align Indels

Requires reference FASTA to determine left-most representation.

## Check for Normalization Issues

```bash
bcftools norm -f reference.fa -c s input.vcf.gz > /dev/null

Use cases

  • Use variant-normalization for genomics and bioinformatics workflows.
  • Apply variant-normalization to sequencing, variant, or omics analysis tasks.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • variant-calling - Generate VCF files
  • filtering-best-practices - Filter after normalization
  • vcf-manipulation - Compare normalized VCFs
  • variant-annotation - Annotate normalized variants

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