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 GPTomics/bioSkills --skill bam-statisticsgit clone --depth 1 https://github.com/GPTomics/bioSkillsWrote 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/gptomics/bioskills/bam-statistics)<a href="https://agentmods.dev/skills/gptomics/bioskills/bam-statistics"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/bam-statistics.svg" alt="Measured on agentmods" 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 | $0.00039 | $0.04338 |
| Opus 5 | $0.00019 | $0.02169 |
| Sonnet 5 | $0.00008 | $0.00868 |
| Haiku 4.5 | $0.00004 | $0.00434 |
Grade A, and why
bio-bam-statistics scanned grade A with 0 findings 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 7d 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.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
Copies of this mod
1 near-identical copy found in the catalogue:
- bio-bam-statistics — 95% identical, 12 lines differ
How it starts
The opening of the file, as written. The whole thing — 426 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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>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.
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.AlignmentFilewithpileup()andget_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 |
| Insert size, MAPQ, error, GC | samtools stats -r ref.fa |
Comprehensive; feeds MultiQC |
| Per-position depth (small region) | samtools depth or pysam pileup |
Slow on full genome |
| Per-position depth (genome-wide) | mosdepth |
3-10x faster than samtools depth |
| Per-region coverage (BED) | mosdepth --by regions.bed |
Production default |
| Coverage histogram / cumulative | mosdepth -t 4 --no-per-base |
Single-pass histogram |
| Breadth at depth thresholds | mosdepth --thresholds 1,10,30,100 |
Standard exome QC |
| Targeted enrichment QC | picard CollectHsMetrics |
PCT_OFF_BAIT, FOLD_80_BASE_PENALTY, AT/GC dropout |
| Cross-sample contamination | verifybamid2, somalier |
FREEMIX < 0.01 expected |
What Each Tool Counts (and Doesn't)
| Counting category | flagstat | stats | idxstats |
|---|---|---|---|
| Primary alignments | in total minus supp |
raw total sequences |
mapped column |
| Secondary | secondary line |
filtered out | counted in mapped |
| Supplementary | supplementary line |
filtered out | counted in mapped |
| Mapping rate denominator | total including supp | primary only | mapped+unmapped |
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.
- 7d ago First seen · 426 lines · 39 tokens per session scan A fb86e671b638
bio-bam-statistics is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 22d ago), licensed MIT. It adds 39 tokens to every session and 4,338 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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