pysam

Topics in the source

• Pysam
• Overview
• When to Use This Skill
• Quick Start
• Installation
• Basic Examples
• Core Capabilities
• 1. Alignment File Operations (SAM/BAM/CRAM)

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. 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 Read alignment file: Read variant file: Query reference sequence: Use the AlignmentFile class to work with aligned sequencing reads. This is appropriate for analyzing mapping results, calculating coverage, extracting reads, or quality control. Common operations: Open and read BAM/SAM/CRAM files Fetch reads from specific genomic regions Filter reads by mapping quality, flags, or other criteria Write filtered or modified alignments Calculate coverage statistics Perform pileup analysis (base-by-base coverage) Access rea

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