bio-variant-calling-joint-calling

npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-variant-calling-joint-calling --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

## Version Compatibility Reference examples tested with: GATK 4.5+, bcftools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - 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. # Joint Calling **"Joint genotype my cohort samples"** → Combine per-sample gVCFs into a single cohort callset with consistent genotyping across all sites, enabling VQSR and population-level analysis. - CLI: `gatk HaplotypeCaller -ERC GVCF` → `gatk GenomicsDBImport` → `gatk GenotypeGVCFs` ## Why Joint Calling? - **Improved sensitivity** - Leverage information across samples - **Consistent genotyping** - Same sites called across all samples - **VQSR eligible** - Requires cohort for machine learning filtering - **Population analysis** - Allele frequencies across cohort ## Workflow Overview ``` Sample BAMs │ ├── HaplotypeCaller (per-sample, -ERC GVCF) │ └── sample1.g.vcf.gz, sample2.g.vcf.gz, ... │ ├── CombineGVCFs or GenomicsDBImport │ └── Combine into cohort database │ ├── GenotypeGVCFs │ └── Joint geno

Generate gVCF for each sample
gatk HaplotypeCaller \
With intervals (faster)
Process all samples
for bam in *.bam; do
done
wait
gatk CombineGVCFs \
Create sample map file
sample1    /path/to/sample1.g.vcf.gz