Skills pysam

📦

pysam

Name: pysam
Author: davila7

Content revision r2 Safe 🌐 Network access📁 Filesystem access⚙️ External commands

使用 Pysam 分析基因組檔案

當檔案格式、索引和座標系統處理不一致時，基因組分析經常會失敗。此 skill 為 Claude、Codex 和 Claude Code 提供針對比對、變異、序列和覆蓋度工作流程的 pysam 專門指引。

Supports: Claude Codex Code(CC)

📊 76 Adequate

Maintain this Skill? Claim it 📊 76 Adequate

Install with my Agent

Copy this request to your Agent. It includes the canonical Skill page and manifest.

Agent request

Review the Skillstore skill "pysam" from https://skillstore.io/skills/davila7-pysam.md and its manifest at https://skillstore.io/api/skills/davila7-pysam/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.

Your Agent should still show its plan and request any confirmation required by the security policy.

Agent-readable resources

Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.

Markdown detail GET /skills/davila7-pysam.md Signed manifest GET /api/skills/davila7-pysam/manifest Signed lockfile GET /api/skills/davila7-pysam/lockfile

Test it

Using "pysam". 審查 chr7:55000000-55200000 範圍覆蓋度的 BAM 檔案工作流程。

Expected outcome:

一份簡潔計畫，涵蓋索引檢查、座標轉換、pileup 或 count_coverage 選擇，以及用於深度審查的摘要指標。

Using "pysam". 將 VCF 篩選為高品質變異，並摘要樣本基因型。

Expected outcome:

逐步篩選方法，包含品質閾值、基因型處理注意事項、標頭保留指引和驗證檢查。

Using "pysam". 使用 FASTA 和 VCF 輸入擷取變異周圍的序列上下文。

Expected outcome:

一個本機工作流程，會檢查參考索引、仔細轉換位置，並回報上下文序列處理決策。

Security Audit

Safe

v10 • 7/23/2026 Open versioned report

All 115 static findings are false positives caused by domain terminology, Markdown formatting, or ordinary genomic file examples. Pysam fetch() reads local indexed data and does not invoke a network API. No prompt injection, exfiltration intent, credential access, reconnaissance, or unsafe command construction was found.

Files scanned

1,836

Lines analyzed

Review items

False positives ignored

Risk Factors

🌐 Network access (42)

📁 Filesystem access (10)

references/alignment_files.md:75 references/common_workflows.md:311 references/common_workflows.md:340 references/common_workflows.md:426 references/sequence_files.md:205 references/sequence_files.md:224 references/sequence_files.md:270 references/sequence_files.md:285 references/sequence_files.md:301 references/variant_files.md:334

⚙️ External commands (45)

No confirmed security findings were detected by the latest completed static and semantic audit. This does not prove the skill has no side effects.

Audited by: codex View Audit History →

Share & cite this report

Share the versioned assessment report, neutral badge, embed card, and citations. Skillstore reports evidence without deciding whether this Skill is safe.

Open versioned report

Copy report link

https://skillstore.io/skills/davila7-pysam/audits/10?utm_source=security_passport&utm_medium=share&utm_campaign=versioned_report

Markdown badge

[![Skillstore security assessment](https://skillstore.io/badges/skills/davila7-pysam/security.svg)](https://skillstore.io/skills/davila7-pysam?utm_source=security_passport_badge)

HTML badge

<a href="https://skillstore.io/skills/davila7-pysam?utm_source=security_passport_badge"><img src="https://skillstore.io/badges/skills/davila7-pysam/security.svg" alt="Skillstore security assessment" loading="lazy"></a>

Embed card

<iframe src="https://skillstore.io/embed/skills/davila7-pysam.html" title="Skillstore Security Assessment" sandbox="allow-popups allow-popups-to-escape-sandbox" loading="lazy" referrerpolicy="no-referrer" width="420" height="180"></iframe>

Academic citations (APA · BibTeX · CFF)

APA citation

davila7. (2026). pysam security audit report (audit version 10) [Author version unspecified]. Skillstore. https://skillstore.io/skills/davila7-pysam/audits/10

BibTeX citation

@techreport{davila7-davila7-pysam-2026,
  author = {davila7},
  title = {pysam security audit report (audit version 10)},
  institution = {Skillstore},
  year = {2026},
  number = {10},
  url = {https://skillstore.io/skills/davila7-pysam/audits/10},
  note = {Author version unspecified}
}

CITATION.cff

cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "pysam security audit report (audit version 10)"
version: "unspecified"
type: report
authors:
  - name: "davila7"
date-released: "2026-07-23"
url: "https://skillstore.io/skills/davila7-pysam/audits/10"
identifiers:
  - type: other
    value: "skillstore:davila7-pysam:audit:10"
    description: "Skillstore immutable audit report identifier"

Compare variants

2 installable variants

Each author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.

Why this variant is first

Highest Skillstore Score

Author / source Skillstore Score Evidence Confidence Skillstore usage Updated

davila7 Recommended Current

davila7-pysam

Skillstore Score 76

Evidence Confidence High

Skillstore usage 15

Updated

2026-09-09

K-Dense-AI

k-dense-ai-pysam

Skillstore Score 38

Evidence Confidence Medium

Skillstore usage 16

Updated

2026-09-09

Skillstore Score

Why this score Evidence Confidence: High

Architecture

Maintainability

Content

Community

Spec Compliance

What You Can Build

建立比對品質檢查

建立 BAM 或 CRAM 工作流程，用於計算 reads、檢查 flags、計算覆蓋度，並正確處理索引。

篩選並摘要變異

處理 VCF 或 BCF 篩選、基因型存取、INFO 欄位、FORMAT 欄位和樣本子集選取。

擷取參考序列和 read 序列

使用 FASTA、FASTQ 和 tabix-indexed 檔案來擷取區域、轉換格式，並準備序列摘要。

Try These Prompts

選擇 pysam 物件

我有 BAM、VCF、FASTA 和 FASTQ 檔案。請說明我應該使用哪些 pysam 類別，以及何時需要索引。

規劃覆蓋度檢查

協助我設計一個 pysam 工作流程，用於從已建立索引的 BAM 檔案計算所選區域的逐鹼基覆蓋度。

安全地篩選變異

指引我依品質、深度、基因型和等位基因頻率篩選 VCF，同時保留標頭資訊。

設計整合管線

設計一個本機 pysam 管線，用 BAM read 支援驗證 VCF 變異，並擷取 FASTA 上下文序列。

Best Practices

在混用 BAM、VCF、BED 和 FASTA 資料之前，確認座標慣例。
在使用區域型查詢之前，建立並驗證索引檔案。
當涉及隱私、同意或合規要求時，請將基因組資料保留在本機。

Avoid

未經存取核准，請勿在可識別的基因組資料上執行範例。
請勿假設 VCF 和 pysam 座標欄位使用相同的索引基準。
當串流處理已足夠時，請勿將大型定序檔案載入記憶體。

Frequently Asked Questions

這個 skill 會安裝 pysam 嗎？

否。它會說明安裝命令和使用模式。使用者或環境必須安裝相依套件。

涵蓋哪些基因組格式？

它涵蓋 SAM、BAM、CRAM、VCF、BCF、FASTA、FASTQ、BED、GTF、GFF 和 tabix-indexed 檔案。

它可以處理真實的基因組檔案嗎？

它可以指引本機程式碼和分析工作流程。它不包含資料集，也不會自行執行工具。

它有助於處理座標系統嗎？

可以。它會強調 0-based pysam 欄位、1-based VCF 位置，以及區域字串差異。

它可以支援私有基因組資料工作嗎？

可以，前提是使用本機檔案。使用者應避免在 prompts 中分享可識別的基因組資料。

Claude、Codex 和 Claude Code 可以使用它嗎？

可以。skill 中繼資料列出對 Claude、Codex 和 Claude Code 的支援。

Developer Details

Author

davila7

License

MIT

Skillstore revision

Version notice

The author did not declare a version.

Repository

https://github.com/davila7/claude-code-templates/tree/main/cli-tool/components/skills/scientific/pysam

Ref

c43861a65bb95efcae259cd161c9d6f4dc7eec6f

Maintenance freshness

7/24/2026

Usage

7 downloads · 191 views

File structure

📁 references/

📄 alignment_files.md

📄 common_workflows.md

📄 sequence_files.md

📄 variant_files.md

📄 SKILL.md

pysam

Install with my Agent

Agent-readable resources

Test it

Security Audit

Risk Factors

Copy report link

Markdown badge

HTML badge

Embed card

APA citation

BibTeX citation

CITATION.cff

Compare variants

Skillstore Score

What You Can Build

建立比對品質檢查

篩選並摘要變異

擷取參考序列和 read 序列

Try These Prompts

Best Practices

Avoid

Frequently Asked Questions

Developer Details

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pysam

Install with my Agent

Agent-readable resources

Test it

Security Audit

Risk Factors

Copy report link

Markdown badge

HTML badge

Embed card

APA citation

BibTeX citation

CITATION.cff

Compare variants

Skillstore Score

What You Can Build

建立比對品質檢查

篩選並摘要變異

擷取參考序列和 read 序列

Try These Prompts

Best Practices

Avoid

Frequently Asked Questions

Developer Details

More from davila7

latex-posters

content-creator

treatment-plans

clinical-reports

exploratory-data-analysis

diffdock

Related Skills

ensembl-database

gtars

pydeseq2

dnanexus-integration

ena-database

pytdc