pysam - a python module for reading, manipulating and writing
genomic data sets.
pysam is a lightweight wrapper of the htslib C-API and provides
facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ
files as well as access to the command line functionality of the
samtools and bcftools packages. The module supports compression and
random access through indexing.
This module provides a low-level wrapper around the htslib C-API as
using cython and a high-level API for convenient access to the data
within standard genomic file formats.