pysam

Overview

Use pysam for low-level, streaming access to HTSlib-supported genomic formats:

• AlignmentFile and AlignedSegment for SAM/BAM/CRAM
• VariantFile, VariantHeader, and VariantRecord for VCF/BCF
• FastaFile for indexed FASTA and FastxFile for sequential FASTA/FASTQ
• TabixFile for BGZF-compressed, tabix-indexed BED/GFF/GTF/custom tables
• pysam.samtools and pysam.bcftools for wrapped command dispatchers

Current upstream baseline: pysam 0.24.1 (7 September 2026), wrapping HTSlib/samtools/bcftools 1.24. Read references/sources.md before updating version-specific guidance.

Installation

Use the pinned release for reproducible work: