CE
cellular-senescence-agent：Cellular senescence analysis：marker scoring，SASP profiling，tissue aging assessment。
FreedomIntelligence/OpenClaw-Medical-Skills查看
流程自动化
FI
filtering-best-practices
维护者 FreedomIntelligence · 最近更新 2026年4月1日
filtering-best-practices。
原始来源
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/filtering-best-practices
- 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
- gatk VariantFiltration \ -R reference.fa \ -V raw_snps.vcf \ -O filtered_snps.vcf \ --filter-expression "QD < 2.0" --filter-name "QD2" \ --filter-expression "FS > 60.0" --filter-name "FS60" \ --filter-expression "MQ < 40.0" --filter-name "MQ40" \ --filter-expression "MQRankSum < -12.5" --filter-name "MQRankSum-12.5" \ --filter-expression "ReadPosRankSum < -8.0" --filter-name "ReadPosRankSum-8" \ --filter-expression "SOR > 3.0" --filter-name "SOR3。
- gatk VariantFiltration \ -R reference.fa \ -V raw_indels.vcf \ -O filtered_indels.vcf \ --filter-expression "QD < 2.0" --filter-name "QD2" \ --filter-expression "FS > 200.0" --filter-name "FS200" \ --filter-expression "ReadPosRankSum < -20.0" --filter-name "ReadPosRankSum-20" \ --filter-expression "SOR > 10.0" --filter-name "SOR10。
原始文档
SKILL.md 摘录
Understanding Quality Metrics
| Metric | Meaning | Good Value |
|---|---|---|
| QD | Quality by Depth | >2 (variant quality normalized by depth) |
| FS | Fisher Strand | <60 SNP, <200 indel (strand bias) |
| MQ | Mapping Quality | >40 (RMS mapping quality) |
| MQRankSum | MQ Rank Sum | >-12.5 (ref vs alt mapping quality) |
| ReadPosRankSum | Read Position | >-8 (position in read bias) |
| SOR | Strand Odds Ratio | <3 SNP, <10 indel (strand bias) |
| DP | Depth | Sample-specific, avoid extremes |
| GQ | Genotype Quality | >20 (confidence in genotype) |
Hard filter (remove variants)
bcftools filter -e 'QUAL<30' input.vcf.gz -o filtered.vcf
Soft filter (mark, don't remove)
bcftools filter -s 'LowQual' -e 'QUAL<30' input.vcf.gz -o marked.vcf
适用场景
- Use filtering-best-practices in 科研工作流 aligned ，支持 this subject area。
- Follow upstream documentation ，用于 full working procedure。
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-calling - Generate VCF files
- variant-calling/gatk-variant-calling - GATK VQSR
- variant-calling/variant-annotation - Annotation after filtering
- variant-calling/vcf-statistics - Evaluate filter effects
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