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variant-annotation

Maintainer FreedomIntelligence · Last updated April 1, 2026

variant-annotation.

OpenClawNanoClawAnalysisReproductionvariant-annotationopenclaw medical skillsadditional scientific toolsvariant

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Annotation Columns (-c)

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

bcftools csq

Simple consequence prediction using GFF annotation.

Use cases

  • Use variant-annotation for genomics and bioinformatics workflows.
  • Apply variant-annotation 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/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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