pysam

What problem does it solve?

This Skill provides a powerful Python interface for efficiently reading, manipulating, and writing complex genomic file formats like SAM/BAM/CRAM, VCF/BCF, and FASTA/FASTQ, streamlining bioinformatics workflows.

Core Features & Use Cases

• Alignment File Operations: Read, write, and process SAM/BAM/CRAM files for alignment analysis, coverage calculation, and quality control.
• Variant File Operations: Work with VCF/BCF files for variant analysis, filtering, and annotation.
• Sequence File Operations: Access FASTA/FASTQ files for reference sequence retrieval and raw read processing.
• Use Case: Analyze sequencing alignment data to identify regions of low coverage or validate variants against a reference genome.

Quick Start

Use the pysam skill to read the first 1000 bases of chromosome 1 from the file 'example.bam'.