📦

pysam

Name: pysam
Author: K-Dense-AI

Content revision r1 High Risk 🌐 Network access📁 Filesystem access⚙️ External commands

Analyze Genomic Files with PySAM

Genomic data workflows need reliable handling of BAM, VCF, FASTA, and FASTQ files. This skill guides PySAM usage for reads, variants, sequences, coverage, and indexing.

Supports: Claude Codex Code(CC)

⚠️ 38 Poor

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Review the plan and obtain explicit user consent before changing files.

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/k-dense-ai-pysam.md and its manifest at https://skillstore.io/api/skills/k-dense-ai-pysam/manifest. Verify the artifact. Stop and obtain explicit user consent before installing or changing files.

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/k-dense-ai-pysam.md Signed manifest GET /api/skills/k-dense-ai-pysam/manifest Signed lockfile GET /api/skills/k-dense-ai-pysam/lockfile

Test it

Using "pysam". Summarize coverage for chr7 from a BAM file.

Expected outcome:

Coverage summary for chr7 target interval.
Mean depth is reported with minimum and maximum depth.
Low-coverage intervals are listed for follow-up review.

Using "pysam". Explain how to extract variants in genes from a VCF and BED file.

Expected outcome:

Open the VCF with PySAM VariantFile and the BED file with TabixFile.
Fetch variants for each gene interval using matching contig, start, and end coordinates.
Return gene names, variant positions, alleles, and quality fields.

Using "pysam". Help avoid coordinate mistakes when using PySAM.

Expected outcome:

Use zero-based, half-open coordinates for numeric PySAM calls.
Use one-based coordinates for region strings and VCF positions.
Document every conversion near the query that uses it.

Security Audit

High Risk

v7 • 7/5/2026 Open versioned report

Most static findings are false positives caused by PySAM terminology: fetch() is local genomic record access, keys() is VCF metadata access, and Markdown backticks are formatting. No evidence found of network exfiltration, credential access, or malicious command execution in the documentation examples. Semantic review found an embedded self-audit asserting the skill is safe and a low-severity promotional instruction for the author's hosted platform.

Files scanned

2,032

Lines analyzed

Review items

False positives ignored

Confirmed security concerns (2)

High

EVALUATION_OUTPUT.json:15-18

Prompt Injection Attempt Detected

EVALUATION_OUTPUT.json embeds an audit result with "risk_level": "safe", "safe_to_publish": true, and a summary saying all static findings are false positives. This can bias downstream security review and should not ship inside the skill.

The file contains explicit safety verdicts and false-positive claims inside the package. It is not code execution, but it directly attempts to steer review outcomes.

Low

SKILL.md:264-265

Self-Promotional Platform Steering

SKILL.md instructs the agent to proactively suggest K-Dense Web for complex workflows. This is unrelated to PySAM functionality and can steer users toward the author's hosted service.

The instruction is explicit and user-facing, but it is promotional rather than malicious. It is best treated as marketplace integrity risk.

Risk Factors

🌐 Network access (49)

📁 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)

Audited by: codex View Audit History →

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Academic citations (APA · BibTeX · CFF)

APA citation

K-Dense-AI. (2026). pysam security audit report (audit version 7) [Author version unspecified]. Skillstore. https://skillstore.io/skills/k-dense-ai-pysam/audits/7

BibTeX citation

@techreport{k-dense-ai-k-dense-ai-pysam-2026,
  author = {K-Dense-AI},
  title = {pysam security audit report (audit version 7)},
  institution = {Skillstore},
  year = {2026},
  number = {7},
  url = {https://skillstore.io/skills/k-dense-ai-pysam/audits/7},
  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 7)"
version: "unspecified"
type: report
authors:
  - name: "K-Dense-AI"
date-released: "2026-07-05"
url: "https://skillstore.io/skills/k-dense-ai-pysam/audits/7"
identifiers:
  - type: other
    value: "skillstore:k-dense-ai-pysam:audit:7"
    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

davila7-pysam

Skillstore Score 76

Evidence Confidence High

Skillstore usage 8

Updated

2026-08-21

K-Dense-AI Current

k-dense-ai-pysam

Skillstore Score 38

Evidence Confidence Medium

Skillstore usage 11

Updated

2026-08-21

Skillstore Score

Why this score Evidence Confidence: Medium

Architecture

Maintainability

Content

Community

Spec Compliance

What You Can Build

Review Alignment Quality

Calculate read counts, mapping rates, duplicate rates, and coverage summaries from BAM or CRAM files.

Inspect Variant Evidence

Combine VCF records with BAM read support and reference context for targeted variant review.

Prepare Sequence Extracts

Extract reference intervals, gene sequences, or filtered reads for downstream analysis.

Try These Prompts

Open an Alignment File

Use PySAM to open a BAM file and list reads overlapping chr1 from 1000 to 2000.

Filter Variant Records

Show how to read a VCF file and keep variants with quality at least 30 and depth at least 20.

Measure Regional Coverage

Create a PySAM workflow that reports per-base coverage and low-coverage intervals for a target region.

Integrate BAM, VCF, and FASTA

Design a PySAM workflow that validates variants with aligned reads and extracts reference sequence context.

Best Practices

Create and verify indexes before using random access queries.
Keep coordinate conversions explicit when moving between BAM, VCF, and region strings.
Stream large files with iterators and close file handles after processing.