How does Pysam handle genomic coordinate systems?

Pysam follows the Python convention of using 0-based, half-open coordinates for programmatic access, while maintaining compatibility with 1-based region strings used by samtools.

What genomic file formats does Pysam support?

Pysam supports all standard high-throughput sequencing formats, including SAM, BAM, and CRAM for alignments, VCF and BCF for variants, and FASTA and FASTQ for sequences.

Does this skill require pre-indexed genomic files?

For random access operations like fetching specific regions, files must be indexed (e.g., .bai for BAM). Pysam includes built-in functions to generate these indices if they are missing.

Can I execute samtools commands directly within this skill?

Yes, Pysam provides a direct wrapper for samtools and bcftools, allowing you to perform operations like sorting, indexing, and merging files without leaving the Python environment.

Pysam Genomic Analysis

Name: Pysam Genomic Analysis
Author: Microck

byMicrock

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Data Science & ML

Processes and analyzes high-throughput genomic datasets including sequence alignments, variants, and reference files using the htslib wrapper.

About

Pysam is a specialized toolkit that provides a Pythonic interface to htslib, allowing for the efficient manipulation of genomic data formats such as SAM, BAM, CRAM, VCF, and FASTA. It is an essential skill for bioinformatics developers building NGS pipelines, performing depth-of-coverage analysis, or filtering large-scale variant sets. By handling complex coordinate systems and providing direct access to samtools and bcftools commands, it simplifies the development of sophisticated scientific computing workflows within Claude Code.

Key Features

Per-base pileup analysis and coverage calculation tools
Comprehensive VCF/BCF variant and genotype processing
Native integration with samtools and bcftools command-line utilities
81 GitHub stars
High-performance random access to FASTA/FASTQ sequences
Read and write SAM/BAM/CRAM alignment files with ease

Use Cases

Building automated Next-Generation Sequencing (NGS) data processing pipelines
Filtering, annotating, and subsetting large-scale genomic variant files
Performing quality control and depth-of-coverage analysis on aligned reads

About

Key Features

Per-base pileup analysis and coverage calculation tools
Comprehensive VCF/BCF variant and genotype processing
Native integration with samtools and bcftools command-line utilities
81 GitHub stars
High-performance random access to FASTA/FASTQ sequences
Read and write SAM/BAM/CRAM alignment files with ease

Use Cases

Building automated Next-Generation Sequencing (NGS) data processing pipelines
Filtering, annotating, and subsetting large-scale genomic variant files
Performing quality control and depth-of-coverage analysis on aligned reads