pysam

SKILL.md

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

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

Quick Start