Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add PKU-YuanGroup/OpenAI4S --skill bio-alignment-files-pileup-generationgit clone --depth 1 https://github.com/PKU-YuanGroup/OpenAI4SWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alignment-files-pileup-generation)<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alignment-files-pileup-generation"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-files-pileup-generation/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/pku-yuangroup/openai4s/bio-alignment-files-pileup-generation"><img src="https://agentmods.dev/badge/skills/pku-yuangroup/openai4s/bio-alignment-files-pileup-generation.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00042 | $0.04101 |
| Opus 5 | $0.00021 | $0.02050 |
| Sonnet 5 | $0.00008 | $0.00820 |
| Haiku 4.5 | $0.00004 | $0.00410 |
Grade A, and why
bio-pileup-generation scanned grade A with 1 finding against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 13d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Makes network callslowCapability
Not a fault in itself. Listed so you know the mod talks to something, and to what.
ref_base = ref.fetch(chrom, pos, pos + 1) This is a copy
97% identical to bio-pileup-generation — 12 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 383 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Version Compatibility
Reference examples tested with: bcftools 1.19+, pysam 0.22+, samtools 1.19+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures - CLI:
<tool> --versionthen<tool> --helpto 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.
Pileup Generation
Generate pileup data for variant calling and position-level analysis.
"Generate pileup from BAM" -> Produce per-position read summaries showing depth, bases, and qualities.
- CLI:
samtools mpileup -f ref.fa input.bam - Python:
bam.pileup(chrom, start, end)(pysam)
"Count alleles at a position" -> Extract per-base read support at a specific genomic coordinate.
- Python: iterate
pileup_column.pileupsand count bases (pysam)
What is Pileup?
Pileup shows all reads covering each position in the reference, used for:
- Variant calling (with bcftools)
- Coverage analysis
- Allele frequency calculation
- SNP/indel detection
samtools mpileup vs bcftools mpileup (Deprecation)
samtools mpileup -g/-u (BCF output for variant calling) was deprecated in samtools 1.9 and removed in 1.15 (the option no longer exists; the usage/manpage directs users to bcftools mpileup) -- the genotype-likelihood code now lives in bcftools mpileup, which keeps mpileup logic versioned alongside bcftools call and avoids version-skew bugs.
| Use case | Recommended tool |
|---|---|
| Quick allele counts at known sites | samtools mpileup or pysam pileup |
| Germline variant calling (small genomes, simple cohorts) | bcftools mpileup -> bcftools call |
| Germline WGS / WES production | DeepVariant or HaplotypeCaller (not mpileup) |
| Somatic SNV/indel | Mutect2 / VarDict / VarScan2 (direct from BAM) |
| Long-read small variants | clair3 / DeepVariant ONT (direct from BAM) |
| Long-read SV | Sniffles / cuteSV (direct from BAM) |
| Ultra-low-frequency (ctDNA / MRD) | fgbio consensus -> bcftools call or hot-spot Mutect2 |
| Per-position allele counts (custom) | pysam pileup |
What ships with it
2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 13d ago First seen · 383 lines · 42 tokens per session scan A 0f195a6ab8b8
bio-pileup-generation is a skill published in the GitHub repository PKU-YuanGroup/OpenAI4S (407 stars, last pushed yesterday), licensed MIT. It adds 42 tokens to every session and 4,101 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 1 finding (makes network calls). It is 97% identical to bio-pileup-generation, differing in 12 lines, and is treated as a copy.
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