PySAM

Pysam is a Python module for reading, manipulating, and writing genomic datasets. It is a lightweight wrapper of the HTSlib API, providing facilities to work with SAM/BAM/CRAM, VCF/BCF, BED, GFF/GTF, FASTA/FASTQ files, and access samtools/bcftools command-line functionality. The module supports compression and random access through indexing. Pysam is actively maintained with regular releases, often wrapping new versions of the underlying htslib, samtools, and bcftools C libraries.