gatk-variant-calling
From the author
GATK Best Practices for germline SNP/indel calling from WGS/WES BAMs. Per-sample HaplotypeCaller GVCFs, GenomicsDBImport, GenotypeGVCFs joint calling, VQSR or hard filters. Requires BWA-MEM2-aligned, markdup, BQSR BAMs. Use DeepVariant for a faster DL alternative; GATK is the NIH/ENCODE standard.
Install
npx skills add jaechang-hits/SciAgent-Skills --skill gatk-variant-calling -a claude-code
Installs to .claude/skills/gatk-variant-calling/ · Each command fetches the skill straight from GitHub with the open skills CLI.
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