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pysam Genomic File Toolkit

Correct, idiomatic pysam workflows for reading, querying, filtering, and writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, and tabix data.

Data & AnalyticsAdvanced★ 33,030⑂ 3,248AI score 9/10Last updated: Aug 9, 2026

What it does

  • Guides Claude to write correct pysam (HTSlib) code for alignment files, variant files, indexed FASTA/FASTQ, and BGZF+tabix tables.
  • Enforces the coordinate contract: numeric APIs are 0-based half-open, region strings are 1-based inclusive — the single most common source of off-by-one bugs.
  • Ships non-destructive helper scripts: inspect_hts.py (metadata-only inspection), alignment_qc.py, variant_summary.py, and filter_alignments.py, all of which refuse to overwrite outputs.
  • Documents real-world pitfalls: CRAM reference resolution, pileup() defaults (base quality, max_depth=8000, truncate=True), header preservation on write, CSI vs BAI indexes, and safe use of the wrapped samtools/bcftools dispatchers.

Who it's for

  • Bioinformaticians and data engineers parsing NGS data in Python.
  • Teams building or maintaining BAM/VCF processing pipelines.
  • samtools CLI users who need the pysam API conventions right the first time.

Examples

  1. "Count primary reads with MAPQ ≥ 30 over chr1:1,000-2,000" → generates fetch code with correct coordinates and flag filters.
  2. "Summarize FILTER values and genotypes in cohort.vcf.gz" → runs python scripts/variant_summary.py cohort.vcf.gz --region chr1:1-1000000.
  3. "My CRAM won't decode" → diagnoses the missing reference and shows reference_filename= versus REF_PATH/REF_CACHE usage.

· · · Install guide · · ·

Try it now, no install

Paste this into Claude to use the skill without installing anything.

Read the instructions in this file and follow them to help me:
https://raw.githubusercontent.com/K-Dense-AI/scientific-agent-skills/HEAD/skills/pysam/SKILL.md

What I want: (describe your task here)

If Claude can't open the link, open it yourself and paste the contents instead.

↓ If it works for you, download the ZIP below and install it. Then it runs on its own — no pasting each time.

Install in the Claude app (no terminal)
  1. Download the ZIP with the button below.
  2. In Claude, open Settings → Capabilities and turn on 'Code execution and file creation'. (one time)
  3. Go to Customize → Skills → + → 'Upload a skill' and upload the ZIP.
↓ Download ZIP
Install in Claude Code

Let Claude do it — paste this into Claude Code

Install the skill I found on Claude Skill Mart.
Copy the skills/pysam folder from the GitHub repo K-Dense-AI/scientific-agent-skills into my ~/.claude/skills/pysam/.
When it's done, tell me in one line what this skill can do.

Install with a command instead

git clone https://github.com/K-Dense-AI/scientific-agent-skills.git /tmp/sas && mkdir -p ~/.claude/skills && cp -r /tmp/sas/skills/pysam ~/.claude/skills/

⚠ This is a third-party skill. Check the source repository before installing.

  1. Open a terminal and create the skills directory: mkdir -p ~/.claude/skills
  2. Clone the repository: git clone https://github.com/K-Dense-AI/scientific-agent-skills.git /tmp/sas
  3. Copy the whole skill folder (the references/ and scripts/ subfolders are required): cp -r /tmp/sas/skills/pysam ~/.claude/skills/
  4. Install the pinned library: uv pip install "pysam==0.24.0" (or pip install pysam==0.24.0). Python 3.8–3.14 is required.
  5. Verify: in Python run import pysam; print(pysam.__version__) and confirm it prints 0.24.0.
  6. Restart Claude Code and try a prompt like "inspect sample.bam and report its sort order and index status".
View source on GitHub ↗License: MIT