pysam

What problem does it solve?

Pysam provides Python bindings to htslib for efficient reading, writing, and querying of SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, plus indexing and pileup analyses, enabling robust NGS pipelines.

Core Features & Use Cases

• Read/write BAM/CRAM/SAM: Access alignments, fetch regions, and compute coverage.
• Variant handling: Query and process VCF/BCF data; count and annotate variants.
• Sequence access: Random access to indexed reference sequences via FastaFile.
• Workflows: End-to-end pipelines combining alignment, variant, and sequence data.

Quick Start

Open a BAM file, fetch reads in a region, and fetch a FASTA sequence from the reference.