bio-phasing-imputation-imputation-qc
Quality control of phasing and imputation results. Filter by INFO scores, assess accuracy, and prepare imputed data for downstream analysis. Use when filtering low-quality imputed variants or validating imputation accuracy before GWAS.
npx skills add BioTender-max/awesome-bio-agent-skills --skill imputation-qc --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: bcftools 1.19+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+ 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. # Imputation QC **"Filter my imputed genotypes by quality"** → Assess imputation accuracy using INFO/R2 scores, filter low-quality imputed variants, and validate against known genotypes before downstream GWAS. - CLI: `bcftools query -f '%CHROM %POS %INFO/R2\n'` to extract quality scores - Python: `pandas` for R2 distribution analysis and threshold selection ## Extract INFO Scores ```bash # Beagle DR2 (dosage R-squared) bcftools query -f '%CHROM\t%POS\t%ID\t%REF\t%ALT\t%INFO/DR2\t%INFO/AF\n' \ imputed.vcf.gz > info_scores.txt # Minimac R2 bcftools query -f '%CHROM\t%POS\t%ID\t%REF\t%ALT\t%INFO/R2\t%INFO/MAF\n' \ imputed.vcf.gz > info_scores.txt # IMPUTE info bcftools query -f '%CHROM\t%POS\t%I
- Version Compatibility
- Extract INFO Scores
- Filter by INFO Score
- INFO Score Distribution
- Summarize Imputation Quality
- Check Concordance with Typed Variants
- Python: Comprehensive QC Report
- Compare Multiple Imputation Runs
- Hardy-Weinberg Filter
- Final QC Pipeline
- Quality Thresholds by Application
- Related Skills
Beagle DR2 (dosage R-squared) bcftools query -f '%CHROM\t%POS\t%ID\t%REF\t%ALT\t%INFO/DR2\t%INFO/AF\n' \ imputed.vcf.gz > info_scores.txt Minimac R2 bcftools query -f '%CHROM\t%POS\t%ID\t%REF\t%ALT\t%INFO/R2\t%INFO/MAF\n' \ IMPUTE info bcftools query -f '%CHROM\t%POS\t%ID\t%INFO\n' imputed.vcf.gz > info_scores.txt Standard threshold for GWAS bcftools view -i 'INFO/DR2 > 0.3' imputed.vcf.gz -Oz -o imputed_r2_03.vcf.gz Strict threshold for fine-mapping
What does the bio-phasing-imputation-imputation-qc skill do?
Quality control of phasing and imputation results. Filter by INFO scores, assess accuracy, and prepare imputed data for downstream analysis. Use when filtering low-quality imputed variants or validating imputation accuracy before GWAS.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill imputation-qc --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.