Skills pysam
📦

pysam

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

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.

6
Files scanned
2,032
Lines analyzed
0
Review items
0
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)
EVALUATION_OUTPUT.json:30 EVALUATION_OUTPUT.json:54 EVALUATION_OUTPUT.json:156 EVALUATION_OUTPUT.json:178 EVALUATION_OUTPUT.json:182 EVALUATION_OUTPUT.json:186 EVALUATION_OUTPUT.json:54 references/alignment_files.md:62 references/alignment_files.md:66 references/alignment_files.md:70 references/alignment_files.md:87 references/alignment_files.md:88 references/alignment_files.md:163 references/alignment_files.md:250 references/alignment_files.md:251 references/common_workflows.md:29 references/common_workflows.md:68 references/common_workflows.md:73 references/common_workflows.md:204 references/common_workflows.md:209 references/common_workflows.md:317 references/common_workflows.md:341 references/common_workflows.md:342 references/common_workflows.md:370 references/common_workflows.md:397 references/common_workflows.md:404 references/sequence_files.md:57 references/sequence_files.md:61 references/sequence_files.md:64 references/sequence_files.md:77 references/sequence_files.md:82 references/sequence_files.md:94 references/sequence_files.md:111 references/sequence_files.md:139 references/sequence_files.md:343 references/sequence_files.md:347 references/sequence_files.md:359 references/sequence_files.md:372 references/variant_files.md:65 references/variant_files.md:69 SKILL.md:42 SKILL.md:60 SKILL.md:83 SKILL.md:164 SKILL.md:166 SKILL.md:167 SKILL.md:181 SKILL.md:207 SKILL.md:262
📁 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)
SKILL.md:30-32 SKILL.md:32-37 SKILL.md:37-45 SKILL.md:45-48 SKILL.md:48-54 SKILL.md:54-57 SKILL.md:57-63 SKILL.md:63-69 SKILL.md:69-80 SKILL.md:80-83 SKILL.md:83-91 SKILL.md:91-102 SKILL.md:102-113 SKILL.md:113 SKILL.md:124-146 SKILL.md:146-164 SKILL.md:164-165 SKILL.md:165-168 SKILL.md:168-170 SKILL.md:170-175 SKILL.md:175 SKILL.md:176-177 SKILL.md:177 SKILL.md:178 SKILL.md:179-181 SKILL.md:181-186 SKILL.md:186-187 SKILL.md:187-188 SKILL.md:188-189 SKILL.md:189-190 SKILL.md:190-191 SKILL.md:191-196 SKILL.md:196-197 SKILL.md:197-200 SKILL.md:200-201 SKILL.md:201-207 SKILL.md:207-209 SKILL.md:209 SKILL.md:217-229 SKILL.md:229-232 SKILL.md:232-237 SKILL.md:237-257 SKILL.md:257-258 SKILL.md:258-259 SKILL.md:259-260
Audited by: codex View Audit History →
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Security Assessment

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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
davila7 Recommended

davila7-pysam

Skillstore Score 76
Evidence Confidence High
Skillstore usage 9
Updated

2026-09-09

K-Dense-AI Current

k-dense-ai-pysam

Skillstore Score 38
Evidence Confidence Medium
Skillstore usage 11
Updated

2026-09-09

Skillstore Score

Why this score Evidence Confidence: Medium
45
Architecture
85
Maintainability
85
Content
70
Community
83
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.

Avoid

  • Loading entire BAM, FASTQ, or VCF files into memory for simple filters.
  • Mixing zero-based and one-based coordinates without comments or tests.
  • Writing output files before validating headers, contigs, and sample names.

Frequently Asked Questions

What genomic files does this skill cover?
It covers SAM, BAM, CRAM, VCF, BCF, FASTA, FASTQ, BED, GTF, and tabix-indexed files.
Does this skill download data from the internet?
No. The documented fetch methods read local indexed genomic files by genomic region.
Why are index files important?
Indexes allow fast random access to large BAM, CRAM, FASTA, VCF, BCF, and tabix files.
Can PySAM replace samtools and bcftools?
PySAM exposes many samtools and bcftools operations, but complex pipelines may still use those tools directly.
What coordinate system should I use?
Numeric PySAM calls usually use zero-based, half-open coordinates. VCF positions and region strings often use one-based coordinates.
Is this skill suitable for clinical decisions?
No. It can support analysis workflows, but clinical interpretation requires validated pipelines and expert review.

Developer Details

Author

K-Dense-AI

License

MIT license

Skillstore revision

r1

Version notice

The author did not declare a version.

Repository

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/pysam

Ref

a25199bc7d6b82598536822d1738eb5d5f54025b

Maintenance freshness

7/18/2026

Usage

7 downloads · 172 views

File structure

📁 references/

📄 alignment_files.md

📄 common_workflows.md

📄 sequence_files.md

📄 variant_files.md

📄 EVALUATION_OUTPUT.json

📄 SKILL.md

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