Pysam is a tool for working with genomic data files. It handles alignment files like BAM and CRAM. It also reads variant files like VCF and sequence files like FASTA. You can use it to extract regions, calculate coverage, and build analysis pipelines. Many scientists and bioinformaticians use pysam for their next generation sequencing work.
With pysam you can quickly fetch reads from a specific chromosome region. You can filter variants by quality. You can also query reference sequences. Everything is done through a simple Python interface. This makes it easy to integrate with other Python scripts.
The library is built on htslib, a widely used C library. It supports tabix-indexed files for fast lookups. You can also run samtools and bcftools commands from Python. Pysam is free to use under the MIT license.
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mkdir -p ~/.claude/skills/pysamProject
mkdir -p .claude/skills/pysamSource Repository
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