bio-variant-calling-filtering-best-practices
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.
npx skills add BioTender-max/awesome-bio-agent-skills --skill filtering-best-practices --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: GATK 4.5+, bcftools 1.19+, numpy 1.26+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Variant Filtering Best Practices ## Filter Selection Decision Tree ``` Is this somatic data? ├── Yes → FilterMutectCalls (GATK), not VQSR or hard filters └── No (germline) → Was DRAGEN-GATK mode used? ├── Yes → Hard filter on QUAL only (DRAGEN QUAL is well-calibrated) └── No → Is dataset large enough for VQSR? ├── Yes (>30 WGS/exomes, human, truth sets available) → VQSR │ └── Large cohort? → Use allele-specific VQSR (-AS flag) └── No → Hard filtering ├── Non-model organism → Hard filtering only (no training resources) └── Targeted panel → Hard filtering (too few variants for VQSR model) ``` VQSR requires a Gaussian mixture model trained on known truth sets (HapMap, 1000G, dbSNP). With fewer than ~30 samples,
- Version Compatibility
- Filter Selection Decision Tree
- GATK Hard Filter Thresholds
- Understanding Quality Metrics
- bcftools filter
- Soft vs Hard Filtering
- Expression Syntax
- Aggregate Functions
- Common bcftools Filters
- bcftools view Filtering
- Filter by Variant Type
- Filter by Region
- Filter by Samples
- Depth Filtering
SNPs gatk VariantFiltration \ Indels 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 Variants failing filter get "LowQual" in FILTER column Include instead of exclude bcftools filter -i 'QUAL>=30' input.vcf.gz -o filtered.vcf
What does the bio-variant-calling-filtering-best-practices skill do?
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.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill filtering-best-practices --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.