{"slug":"jaechang-hits-vcf-variant-filtering","source_name":"jaechang-hits/vcf-variant-filtering","name":"Jaechang Hits/Vcf Variant Filtering","description":"Guide to quality filtering raw VCF files before computing summary stats (Ts/Tv ratio, variant counts, AF distributions). Covers detecting raw VCFs via FILTER column and QUAL inspection, QUAL-based filtering with bcftools, Ts/Tv interpretation, and when NOT to filter. Read before any variant-level QC task. See bcftools-variant-manipulation for advanced filters, gatk-variant-calling for caller config, samtools-bam-processing for upstream alignment QC.","version":2,"lift":{"pass_rate_delta_pts":17.39,"pass_rate_pct":100,"total_cases":23,"passed_cases":23,"tokens_delta_pct":200.9,"turns_delta_pct":0,"verdict":"pass","benchmark_model":"gemini-3.6-flash","grading_method":"judged","completed_at":"2026-08-24T12:04:14.525571+00:00"},"skill_score":1,"benchmark_models":[{"model":"gemini-3.6-flash","headline":true,"delta_pts":17.39,"with_pass_pct":100,"without_pass_pct":82.6,"tokens_delta_pct":200.9,"turns_delta_pct":0,"total_cases":23,"cases_aggregated":23,"verdict":"pass","never_hurt":true,"completed_at":"2026-08-24T12:04:14.525571+00:00","run_id":"01b51cd9-e331-49d9-8d9b-5a3d10becc43","latest_attempt":{"id":"01b51cd9-e331-49d9-8d9b-5a3d10becc43","runner_model":"gemini-3.6-flash","overall_verdict":"pass","completed_at":"2026-08-24T12:04:14.525571+00:00","gate":null},"version_number":1,"is_latest_version":false,"gate":null}],"trust":{"skill_safety":"passed","safety_status":"clean","intent_verdict":null,"content_status":"clean","indexable":true},"license":"CC-BY-4.0","install_count":0,"total_uses":43,"total_users":3,"manifest_hash":"176187cbb35bbdeefc7e7c2803d2c87b408b049208d099c75639c148fdcc7b09","install_name":"jaechang-hits-vcf-variant-filtering","version_id":"c79dcc06-53fb-474e-80c0-195ffc928759","body_sha256":"176187cbb35bbdeefc7e7c2803d2c87b408b049208d099c75639c148fdcc7b09","render_hash":"ea67124fd335cb9988e8f395c3bef4811ba65c8bbab6a6b3a639053caab7ed77","raw_url":"https://app.decimal.ai/s/jaechang-hits-vcf-variant-filtering/SKILL.md","scorecard_url":"https://app.decimal.ai/skills/jaechang-hits-vcf-variant-filtering"}