Individual skill
pysam
Provides Python/HTSlib workflows for genomic files. Used 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.
skills/pysam/SKILL.md
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- Last checked
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- License
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# pysam
## Overview
Use pysam for low-level, streaming access to HTSlib-supported genomic formats:
- `AlignmentFile` and `AlignedSegment` for SAM/BAM/CRAM
- `VariantFile`, `VariantHeader`, and `VariantRecord` for VCF/BCF
- `FastaFile` for indexed FASTA and `FastxFile` for sequential FASTA/FASTQ
- `TabixFile` for BGZF-compressed, tabix-indexed BED/GFF/GTF/custom tables
- `pysam.samtools` and `pysam.bcftools` for wrapped command dispatchers
Current upstream baseline: **pysam 0.24.1** (7 September 2026), wrapping
HTSlib/samtools/bcftools 1.24. Read `references/sources.md` before updating