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Timothy Kassis
2025-10-21 12:50:07 -07:00
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scientific-packages/pysam/SKILL.md
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@@ -7,18 +7,11 @@ description: "Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF
## Overview
Pysam is a Python module for reading, manipulating, and writing genomic datasets. It provides a Pythonic interface to the htslib C-API, supporting multiple genomic file formats commonly used in bioinformatics and computational biology.
Pysam is a Python module for reading, manipulating, and writing genomic datasets. Read/write SAM/BAM/CRAM alignment files, VCF/BCF variant files, and FASTA/FASTQ sequences with a Pythonic interface to htslib. Query tabix-indexed files, perform pileup analysis for coverage, and execute samtools/bcftools commands.
**Key capabilities:**
- Read/write SAM/BAM/CRAM alignment files (aligned sequencing reads)
- Read/write VCF/BCF variant call files (genetic variants)
- Access FASTA reference sequences with random access
- Read FASTQ files (raw sequencing reads with quality scores)
- Query tabix-indexed files (BED, GTF, GFF)
- Perform pileup analysis for coverage calculations
- Execute samtools and bcftools commands from Python
## When to Use This Skill
**When to use this skill:**
This skill should be used when:
- Working with sequencing alignment files (BAM/CRAM)
- Analyzing genetic variants (VCF/BCF)
- Extracting reference sequences or gene regions