{"slug":"jaechang-hits-gatk-variant-calling","source_name":"jaechang-hits/gatk-variant-calling","name":"Jaechang Hits/Gatk Variant Calling","description":"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.","version":1,"lift":{"pass_rate_delta_pts":8.33,"pass_rate_pct":100,"total_cases":24,"passed_cases":24,"tokens_delta_pct":313.5,"turns_delta_pct":0,"verdict":"pass","benchmark_model":"gemini-3.6-flash","grading_method":"judged","completed_at":"2026-08-24T11:56:10.391770+00:00"},"skill_score":1,"benchmark_models":[{"model":"gemini-3.6-flash","headline":true,"delta_pts":8.33,"with_pass_pct":100,"without_pass_pct":91.7,"tokens_delta_pct":313.5,"turns_delta_pct":0,"total_cases":24,"cases_aggregated":24,"verdict":"pass","never_hurt":true,"completed_at":"2026-08-24T11:56:10.391770+00:00","run_id":"a0f52841-7a90-418e-8980-e882f2129d7f","version_number":1,"is_latest_version":true,"gate":null}],"trust":{"skill_safety":"passed","safety_status":"clean","intent_verdict":"safe","content_status":"clean","indexable":true},"license":"BSD-3-Clause","install_count":0,"manifest_hash":"272d8e6aa43ad58459b9898d3cd156705d9e8c1419233b6b64dc4f610fb39c2c","raw_url":"https://app.decimal.ai/s/jaechang-hits-gatk-variant-calling/SKILL.md","scorecard_url":"https://app.decimal.ai/skills/jaechang-hits-gatk-variant-calling"}