{"slug":"jaechang-hits-samtools-bam-processing","source_name":"jaechang-hits/samtools-bam-processing","name":"Jaechang Hits/Samtools Bam Processing","description":"CLI toolkit for SAM/BAM/CRAM: sort, index, convert, filter, QC alignments. Core commands: view, sort, index, flagstat, stats, depth, markdup, merge. Required between alignment and variant/peak calling. Use pysam for Python-native BAM access; deeptools for normalized coverage tracks.","version":1,"lift":{"pass_rate_delta_pts":4.55,"pass_rate_pct":100,"total_cases":22,"passed_cases":22,"tokens_delta_pct":359.9,"turns_delta_pct":0,"verdict":"pass","benchmark_model":"gemini-3.6-flash","grading_method":"judged","completed_at":"2026-08-23T23:53:35.771177+00:00"},"skill_score":1,"benchmark_models":[{"model":"gemini-3.6-flash","headline":true,"delta_pts":4.55,"with_pass_pct":100,"without_pass_pct":95.5,"tokens_delta_pct":359.9,"turns_delta_pct":0,"total_cases":22,"cases_aggregated":22,"verdict":"pass","never_hurt":true,"completed_at":"2026-08-23T23:53:35.771177+00:00","run_id":"8ca7f242-793a-4e9e-9e07-85ec34c72833","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":"MIT","install_count":0,"manifest_hash":"9f1e1ab0c79b9631d2cd36c3f7158c6c6fae84031ca6590b7209762175dd77b9","raw_url":"https://app.decimal.ai/s/jaechang-hits-samtools-bam-processing/SKILL.md","scorecard_url":"https://app.decimal.ai/skills/jaechang-hits-samtools-bam-processing"}