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