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bio-variant-annotation

Maintainer FreedomIntelligence · Last updated April 1, 2026

Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical significance. Use when annotating variants with functional and clinical information.

OpenClawNanoClawAnalysisReproductionbio-variant-annotation🧬 bioinformatics (gptomics bio-* suite)bioinformatics — clinical databases & variant analysiscomprehensive

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • bcftools annotate -a regions.bed.gz -c CHROM,FROM,TO,INFO/REGION \ -h <(echo '##INFO=<ID=REGION,Number=1,Type=String,Description="Region name">') \ input.vcf.gz -Oz -o annotated.vcf.gz.
  • bcftools annotate -a annotations.tab.gz -c CHROM,POS,INFO/SCORE \ -h <(echo '##INFO=<ID=SCORE,Number=1,Type=Float,Description="Custom score">') \ input.vcf.gz -Oz -o annotated.vcf.gz.

Source Doc

Excerpt From SKILL.md

Tool Comparison

ToolBest ForSpeedOutput
bcftools csqSimple consequence predictionFastVCF
VEPComprehensive with pluginsModerateVCF/TXT
SnpEffFast batch annotationFastVCF
ANNOVARFlexible databasesModerateTXT

bcftools annotate

Goal: Add or remove INFO/ID annotations from external databases using bcftools.

Approach: Match variants by position and allele against annotation VCF/BED/TAB files, copying specified columns.

"Add rsIDs to my VCF from dbSNP" → Match variant positions against a database and copy identifiers or annotation fields into the VCF.

Annotation Columns (-c)

OptionDescription
IDCopy ID column
INFOCopy all INFO fields
INFO/TAGCopy specific INFO field
+INFO/TAGAdd to existing values

Use cases

  • Use when annotating variants with functional and clinical information.

Not for

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

Upstream Related Skills

  • variant-calling/variant-normalization - Normalize before annotating
  • variant-calling/filtering-best-practices - Filter by annotations
  • variant-calling/vcf-basics - Query annotated fields
  • database-access/entrez-fetch - Download annotation databases

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