bio-variant-calling-joint-calling

npx skills add BioTender-max/awesome-bio-agent-skills --skill 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 Matters Single-sample calling discards cross-sample evidence that is critical for accurate genotyping: - **Statistical power from shared evidence** - A site with 2 alt reads in one sample is borderline and would typically be missed. If 50 other samples in the cohort also show 2 alt reads at that site, the evidence is overwhelming and the variant is clearly real. Joint calling aggregates this weak-per-sample signal into strong cohort-level evidence. - **Genotype refinement via cohort priors** - Ind

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