Data & ReproClinical MedicineFreedomIntelligence/OpenClaw-Medical-SkillsData & Reproduction

bio-variant-calling-filtering-best-practices

Maintainer FreedomIntelligence · Last updated April 1, 2026

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.

OpenClawNanoClawAnalysisReproductionbio-variant-calling-filtering-best-practices🧬 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-calling-filtering-best-practices

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

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".

Source Doc

Excerpt From SKILL.md

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.