数据与复现临床医学与医药FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-variant-calling-filtering-best-practices

维护者 FreedomIntelligence · 最近更新 2026年4月1日

Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretation for SNPs and indels. Use when filtering variants using GATK best practices.

OpenClawNanoClaw分析处理复现实验bio-variant-calling-filtering-best-practices🧬 bioinformatics (gptomics bio-* suite)bioinformatics — clinical databases & variant analysiscomprehensive

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

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

2 min

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

GATK Hard Filter Thresholds

Goal: Apply GATK-recommended annotation thresholds to separate true variants from artifacts.

Approach: Use VariantFiltration with per-metric filter expressions for SNPs and indels separately.

"Filter my variants using GATK best practices" → Apply fixed annotation thresholds (QD, FS, MQ, SOR, RankSum) to flag low-quality variants.


## 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) |

## bcftools filter

**Goal:** Filter variants using bcftools expression syntax with soft or hard removal.

**Approach:** Use -e (exclude) or -i (include) with expressions on QUAL, INFO, and FORMAT fields; use -s for soft filtering.