All skills & plugins / Scientific Agent Skills (K-Dense)

pysam

Provides Python/HTSlib workflows for genomic files. Used when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam, including pileup, coverage, indexing, and CRAM references.

Type: Skill by K-Dense Inc.
Catalog: Scientific Agent Skills (K-Dense)
Source: K-Dense-AI/scientific-agent-skills/skills/pysam (14 files scanned)
Install and details: Agent Skills Index entry
License: MIT (SKILL.md frontmatter)
Signals: Pre-approved shellBundled scriptsNetwork calls in code

Pre-approved tools

Shell (any command). Tools listed in allowed-tools (or an agent's tools) can be used without a permission prompt while the skill is active, depending on your agent and settings.

Kind	Tools
read/search	`Read`
write/edit files	`WriteEdit`
shell, any command	`Bash`

Declared in pysam/SKILL.md.

Hooks

No hooks.

MCP servers and apps

None.

Bundled code

4 code files (Python):

Network calls

3 files with a network call pattern. First match per file:

skills/pysam/scripts/alignment_qc.py:5

uses fetch(until_eof=True) and needs no index. --region is a 1-based inclusive

skills/pysam/scripts/variant_summary.py:96
```
return variants.fetch(region=region)
```
skills/pysam/scripts/filter_alignments.py:143
```
return alignments.fetch(until_eof=True)
```

Starts other programs

No subprocess, exec or eval pattern found.

Credentials referenced

No key, token or secret environment variable found in code or MCP config.

Static scan of commit 5f2bc03 on 2026-10-27. Signals are patterns found in the files, not a verdict: a network call can be the whole point of a skill. Read the linked lines before you decide. How the scan works.