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数据与复现
BI
bio-variant-annotation
维护者 FreedomIntelligence · 最近更新 2026年4月1日
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.
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-variant-annotation
- 维护者
- FreedomIntelligence
- 许可
- MIT
- 最近更新
- 2026年4月1日
技能摘要
来自 SKILL.md 的关键信息
核心说明
- bcftools annotate - regions.bed.gz -c CHROM，，面向，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 - 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。
原始文档
SKILL.md 摘录
Tool Comparison
| Tool | Best For | Speed | Output |
|---|---|---|---|
| bcftools csq | Simple consequence prediction | Fast | VCF |
| VEP | Comprehensive with plugins | Moderate | VCF/TXT |
| SnpEff | Fast batch annotation | Fast | VCF |
| ANNOVAR | Flexible databases | Moderate | TXT |
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)
| Option | Description |
|---|---|
ID | Copy ID column |
INFO | Copy all INFO fields |
INFO/TAG | Copy specific INFO field |
+INFO/TAG | Add to existing values |
适用场景
- 适合在annotating variants ，支持 functional 、 clinical information时使用。
不适用场景
- Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。
上游相关技能
- 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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