> ## Documentation Index
> Fetch the complete documentation index at: https://docs.kalarislabs.com/llms.txt
> Use this file to discover all available pages before exploring further.

# pysam — AI agent skill for life sciences

> Python/HTSlib workflows for genomic files.

# `pysam`

> Python/HTSlib workflows for genomic files. Use 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.

**Category:** [life-sciences](/research-agent-skills/skills#life-sciences) · **License:** MIT · **Version:** 2.1

## Install

```bash theme={null}
npx research-agent-skills install pysam
npx skills add KalarisLabs/research-agent-skills --skill pysam
```

## When to use it

Python/HTSlib workflows for genomic files. Use 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.

## Full playbook

Read [SKILL.md](https://github.com/KalarisLabs/research-agent-skills/blob/main/skills/pysam/SKILL.md) for the complete workflow, references and any scripts. The agent installer copies the full skill folder.


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