Individual skill
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.
plugins/KalarisLabs/research-agent-skills/skills/pysam/SKILL.md
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- Last checked
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- Nov 6, 2026
- License
- Apache-2.0
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- sam/bam,-vcf,-genomics,-sequencing-data,-bioinformatics Declared skill tag
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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 0.24.0** (27 April 2026), wrapping
HTSlib/samtools/bcftools 1.23.1. Read `references/sources.md` before updating