pysam

Name: pysam
Author: K-Dense-AI

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.

pysam

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---
name: pysam
description: Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
license: MIT license
metadata:
    skill-author: K-Dense Inc.
---

# Pysam

## Overview

Pysam is a Python module for reading, manipulating, and writing genomic datasets. Read/write SAM/BAM/CRAM alignment files, VCF/BCF variant files, and FASTA/FASTQ sequences with a Pythonic interface to htslib. Qu

How to Use

Recommended: Install to project (local)

mkdir -p .claude/skills
curl -o .claude/skills/pysam.md \
  https://raw.githubusercontent.com/K-Dense-AI/claude-scientific-skills/main/scientific-skills/pysam/SKILL.md

Skill is scoped to this project only. Add .claude/skills/ to your .gitignoreif you don't want to commit it.

Alternative: Clone full repo

git clone https://github.com/K-Dense-AI/claude-scientific-skills

Then reference at scientific-skills/pysam/SKILL.md