pysam
Reads and writes BAM, CRAM and VCF files from Python through HTSlib.
Install
Ships scriptsgh skill install K-Dense-AI/scientific-agent-skills pysam
Reading, querying, filtering or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ or tabix-indexed files; pileup and coverage work.
- Author
- K-Dense Inc.
- License
- MIT
Covers the streaming, index-aware side of genomic file handling: region queries, pileups, coverage, flag and quality filtering, and writing new files without losing the header. Format, sort order, index and coordinate convention have to be settled before any code is written, because mixing zero-based Python coordinates with one-based region strings is the usual source of silently wrong results. Four bundled scripts inspect an unfamiliar file, summarize alignment QC, filter reads and summarize variants. Guidance is pinned to pysam 0.24.0 over HTSlib 1.23.1 and carries a separate migration note.
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