pysam
Python/HTSlib workflows for genomic files. Use when reading, querying, filtering, or writing SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, or tabix data with pysam, including pileup, coverage, indexing, and CRAM references.
- Version
- 2.1
- License
- MIT
- Compatibility
- Requires Python 3.8–3.14 and pysam 0.24.0. Bundled scripts use local files. CRAM decoding may require the matching reference FASTA or an explicitly configured REF_PATH/REF_CACHE.
Pinned to revision 70a605012eee, so it is the text this page describes rather than whatever the author pushed since.
Pre-approved tools experimental
Experimental field. Support varies between clients, so this list is what the author declared, not what your client will enforce.
- Read
- Write
- Edit
- Bash
Files
- skills/pysam/SKILL.md
- skills/pysam/references/alignment_files.md
- skills/pysam/references/api_reference.md
- skills/pysam/references/common_workflows.md
- skills/pysam/references/coordinates_and_indexing.md
- skills/pysam/references/cram_and_performance.md
- skills/pysam/references/migration_to_0_24.md
- skills/pysam/references/sequence_files.md
- skills/pysam/references/sources.md
- skills/pysam/references/variant_files.md
- skills/pysam/scripts/alignment_qc.py
- skills/pysam/scripts/filter_alignments.py
- skills/pysam/scripts/inspect_hts.py
- skills/pysam/scripts/variant_summary.py
Every link opens the file at its source, pinned to the revision this page describes.