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pysam

Maintainer K-Dense Inc. · Last updated April 1, 2026

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. Query tabix-indexed files, perform pileup analysis for coverage, and execute samtools/bcftools commands.

Claude CodeOpenClawNanoClawWritingSubmissionpysambioinformaticspackagebioinformatics & genomics

Original source

K-Dense-AI/claude-scientific-skills

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/pysam

Maintainer: K-Dense Inc.
License: MIT license
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

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. Query tabix-indexed files, perform pileup analysis for coverage, and execute samtools/bcftools commands.
samfile = pysam.AlignmentFile("example.bam", "rb") for read in samfile.fetch("chr1", 1000, 2000): print(f"{read.query_name}: {read.reference_start}") samfile.close() python.

Source Doc

Excerpt From SKILL.md

When to Use This Skill

This skill should be used when:

Working with sequencing alignment files (BAM/CRAM)
Analyzing genetic variants (VCF/BCF)
Extracting reference sequences or gene regions
Processing raw sequencing data (FASTQ)
Calculating coverage or read depth
Implementing bioinformatics analysis pipelines
Quality control of sequencing data
Variant calling and annotation workflows

Basic Examples

Read alignment file:

import pysam

## Open VCF file and iterate variants

vcf = pysam.VariantFile("variants.vcf")
for variant in vcf:
    print(f"{variant.chrom}:{variant.pos} {variant.ref}>{variant.alts}")
vcf.close()
python