Pysam

If you're working with genomic data in Python, this is the standard tool for reading and writing alignment files (BAM/CRAM), variant files (VCF/BCF), and reference sequences (FASTA/FASTQ). It wraps htslib so you get the full samtools/bcftools ecosystem with a Pythonic interface. The main thing to watch for is the coordinate system: it uses 0-based half-open intervals except when you pass region strings to fetch(), which are 1-based like samtools. You'll need index files for random access, and the documentation here covers the core workflows like calculating coverage, validating variants against reads, and filtering based on quality metrics. It's mature, well maintained, and handles the file format complexity so you don't have to.

Install to Claude Code

npx -y skills add davila7/claude-code-templates --skill pysam --agent claude-code