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FreedomIntelligence/OpenClaw-Medical-SkillsView
Data & Repro
BI
bio-phasing-imputation-imputation-qc
Maintainer FreedomIntelligence · Last updated April 1, 2026
QC imputed data: R² filter, INFO score, allele concordance.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-phasing-imputation-imputation-qc
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- 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.
- 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.
Source Doc
Excerpt From SKILL.md
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
bcftools view -i 'INFO/DR2 > 0.8' imputed.vcf.gz -Oz -o imputed_r2_08.vcf.gz
Use cases
- Use bio-phasing-imputation-imputation-qc for genomics and bioinformatics workflows.
- Apply bio-phasing-imputation-imputation-qc to sequencing, variant, or omics analysis tasks.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- phasing-imputation/genotype-imputation - Generate imputed data
- variant-calling/filtering-best-practices - VCF filtering operations
- population-genetics/association-testing - GWAS with imputed data
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