A Python interface to HTSlib for reading and writing common genomics files. HTSlib is a widely used library for sequence alignments, variants, reference sequences, and indexed genomic tables.

It is for working with SAM, BAM, CRAM, VCF, BCF, FASTA, FASTQ, and tabix-indexed files, including alignment queries, variant processing, indexing, and coverage analysis.

Genomic files can be large and compressed, so loading everything into memory is often impractical. This toolkit supports streaming, indexed queries, filtering, pileups, and coverage calculations.

pysam — Skill for Claude Code by agentlas-ai/agentlas-desktop

Install

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.

Any agent

npx skills add agentlas-ai/agentlas-desktop --skill pysam

Clone the repo

git clone --depth 1 https://github.com/agentlas-ai/agentlas-desktop

Made for: Claude Code.

Wrote 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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/pysam/github.svg)](https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/pysam)

Your own site

<a href="https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/pysam"><img src="https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/pysam/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/agentlas-ai/agentlas-desktop/pysam"><img src="https://agentmods.dev/badge/skills/agentlas-ai/agentlas-desktop/pysam.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 64 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 3,175 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 1 finding. A grade says what 26 rules found in the file — not that it is safe.

Origin 100% copy Near-identical to another mod in the catalogue.

Token cost

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	$0.00064	$0.03175
Opus 5.5	$0.00026	$0.01270
Sonnet 5.5	$0.00013	$0.00635
Haiku 4.5	$0.00006	$0.00317

Measured 1mo ago against content hash 4cbfdbd80b4a, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

pysam scanned grade A with 1 finding 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 1mo ago.

The scan reads SKILL.md. This mod also ships 4 executable files (scripts/alignment_qc.py, scripts/filter_alignments.py, scripts/inspect_hts.py, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

bam.fetch(region="chr1:100-199") # 1-based inclusive

Origin

This is a copy

100% identical to pysam — 50 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.

plugins/agentlas-science-skills/skills/pysam/SKILL.md · 348 lines

How it starts

The opening of the file, as written. The whole thing — 348 lines — stays where its author put it; the contents beside it link to each section on GitHub.

pysam

Overview

Use pysam for low-level, streaming access to HTSlib-supported genomic formats:

AlignmentFile and AlignedSegment for SAM/BAM/CRAM
VariantFile, VariantHeader, and VariantRecord for VCF/BCF
FastaFile for indexed FASTA and FastxFile for sequential FASTA/FASTQ
TabixFile for BGZF-compressed, tabix-indexed BED/GFF/GTF/custom tables
pysam.samtools and pysam.bcftools for wrapped command dispatchers

Current upstream baseline: pysam 0.24.0 (27 April 2026), wrapping HTSlib/samtools/bcftools 1.23.1. Read references/sources.md before updating version-specific guidance.

Installation

Use the pinned release for reproducible work:

uv pip install "pysam==0.24.0"

Confirm the runtime:

import pysam

print(pysam.__version__)           # 0.24.0
print(pysam.__samtools_version__)  # 1.23.1

Prebuilt wheels are available for supported macOS and Linux platforms. A source build needs a C compiler and HTSlib build dependencies; read the official installation guide linked from references/sources.md.

First Decide

Before writing code:

Identify the real format, compression, sort order, and available index.
Decide whether coordinates are numeric Python coordinates or a region string. Do not mix them.
For CRAM, identify the exact reference assembly and FASTA.
Prefer indexed region access; use sequential iteration only when intended.
Preserve headers when writing and write to a new path by default.
State filtering semantics: mapping/base quality, flags, overlap handling, duplicate handling, and pileup depth cap.

For unfamiliar files, start with the bundled read-only inspector:

python scripts/inspect_hts.py sample.bam
python scripts/inspect_hts.py cohort.vcf.gz
python scripts/inspect_hts.py reference.fa

Bundled Scripts

Script	Purpose	Typical call
`scripts/inspect_hts.py`	Metadata-only inspection for alignment, variant, FASTA, FASTQ, and tabix files	`python scripts/inspect_hts.py sample.cram --reference ref.fa`
`scripts/alignment_qc.py`	Streaming aggregate read/QC counts as JSON	`python scripts/alignment_qc.py sample.bam --max-records 100000`
`scripts/variant_summary.py`	Streaming variant, FILTER, and genotype summary as JSON	`python scripts/variant_summary.py cohort.vcf.gz --region chr1:1-1000000`
`scripts/filter_alignments.py`	Filter SAM/BAM/CRAM without changing record order	`python scripts/filter_alignments.py input.bam output.bam --exclude-secondary`

Read the full file on GitHub · 348 lines

Files

What ships with it

13 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.

Changes

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.

1mo ago First seen · 348 lines · 64 tokens per session scan A 4cbfdbd80b4a

Subscribe to this mod's changes

pysam is a skill published in the GitHub repository agentlas-ai/agentlas-desktop (6 stars, last pushed yesterday), licensed Apache-2.0. It adds 64 tokens to every session and 3,175 once invoked, about $0.0003 per session on Opus 5.5. A static security scan graded it A with 1 finding (makes network calls). It is 100% identical to pysam, differing in 50 lines, and is treated as a copy.

Scientific agentlas ai-agents electron macos mcp

tbtools

Use when the user asks about TBtools, TBtools-II, TBtools RPC API, TBtools CLI, or bioinformatics operations available through TBtools such as sequence manipulation, BLAST, GFF/GTF/GXF processing, expression tables, heatmaps, trees, MCScanX, DIAMOND, HMMER, MUSCLE, and IQ-TREE.

xuzhougeng/wispterm · 77 tokens

electron-expert

Expert in Electron framework, desktop app development, IPC, and cross-platform packaging. Use when the user mentions desktop, Node.js, cross platform, Windows, macOS, or Linux, or when the task involves Electron Architecture, Process Types, IPC Communication, or App Lifecycle.

personamanagmentlayer/pcl · 59 tokens

research-orchestrator

Becomes a principal research scientist who orchestrates deep, multi-source research by coordinating evidence gathering, grading source quality, and synthesizing findings with explicit confidence levels. Use when the user needs a comprehensive research report on a complex topic, evidence-based analysis with source…

FerroxLabs/wayland · 109 tokens

autoresearch

Run an auto research / autoresearch loop for measurable improvements. Use when optimizing a skill, agent, prompt, code path, benchmark, or other target with a mechanical metric: baseline, mutate one thing, verify, keep or discard, log, chart progress, and optionally save improved custom skills or agents through Open…

joe-broadhead/open-cowork · 0 tokens

architecture-diagram

How to draw and maintain the architecture diagram Ensemblr keeps for a workspace — ensemblrgetarchitecturediagram to fetch the stored one (it answers with null when nobody has drawn this workspace yet), the IR shape, how to derive it from the codebase, and ensemblrupdatearchitecturediagram to store it. Read this when…

ensemblr-hq/ensemblr · 94 tokens

scaffold-lean-library

Scaffold a Lean 4 library with Mathlib or PFR, Lake tests, and CI. Use for "new Lean project"; to edit Lean, use write-lean-code.

cboone/agent-harness-plugins · 43 tokens

pysam

Getting it into your agent

Wrote this? Show the measurements

What it costs to keep this loaded

Grade A, and why

Makes network callslowCapability

This is a copy

How it starts

pysam

Overview

Installation

First Decide

Bundled Scripts

What ships with it

What this file has done since we first saw it

Other skills, from other repositories

tbtools

electron-expert

research-orchestrator

autoresearch

architecture-diagram

scaffold-lean-library