bio-gatk-variant-calling

npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-gatk-variant-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. # GATK Variant Calling GATK HaplotypeCaller is the gold standard for germline variant calling. This skill covers the GATK Best Practices workflow. ## Prerequisites BAM files should be preprocessed: 1. Mark duplicates 2. Base quality score recalibration (BQSR) - optional but recommended ## Single-Sample Calling **Goal:** Call germline SNPs and indels from a single sample using HaplotypeCaller. **Approach:** Run local de novo assembly of haplotypes in active regions to detect variants with optional annotation enrichment. **"Call variants from my BAM file using GATK"** → Perform local haplotype assembly and genotyping on aligned reads using HaplotypeCaller. ### Basic HaplotypeCaller ```bash gatk HaplotypeCaller \ -R reference.fa \ -I sample.bam \ -O sample.vcf.gz ``` ### With Standard Annotations ```bash

gatk HaplotypeCaller \
Create sample map file
sample1    /path/to/sample1.g.vcf.gz
sample2    /path/to/sample2.g.vcf.gz
gatk GenomicsDBImport \
gatk CombineGVCFs \
From GenomicsDB
gatk GenotypeGVCFs \
From combined GVCF
Build SNP model