bio-bam-statistics SKILL.md skillA
bio-bam-statistics from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-bam-statistics@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-alignment-files-bam-statistics/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 15,700 bytes
- Repository stars
- 662
- License
- MIT
Generate alignment statistics using samtools flagstat, stats, depth, coverage, and mosdepth. Use when assessing alignment quality, calculating coverage, or generating QC reports.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
## Version Compatibility Reference examples tested with: pysam 0.22+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - 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. # BAM Statistics **"Get alignment statistics and coverage from my BAM file"** -> Generate read counts, mapping rates, per-chromosome statistics, depth profiles, and coverage summaries. - CLI: `samtools flagstat`, `samtools stats`, `samtools depth`, `samtools coverage` (samtools) - Python: `pysam.AlignmentFile` with `pileup()` and `get_index_statistics()` (pysam) Generate alignment statistics using samtools and pysam. ## Quick Summary Commands | Question | Best tool | Why | |----------|-----------|-----| | Quick read counts by FLAG category | `samtools flagstat` | Fast; counts secondary+supp in totals | | Per-chromosome counts | `samtools idxstats` | Fast (needs index); **counts secondary+supp** | …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-bam-statistics@sha256:15655223371768a9The line at the top of this page pins the label git:20260821.2d1b678, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_sardn3brxxsarzhp)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
Audit of the latest version
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- pass: No script tag
Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_sardn3brxxsarzhp GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-bam-statistics GET https://markdownregistry.com/api/v1/blob/15655223371768a9af117a854a477f49fdf2c6e3a2450ac879a83414a404dbe1
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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