How do I calculate sequencing coverage with Pysam?

You can use the pileup() method for base-by-base coverage analysis or the count() method for a quick count of reads overlapping a specific genomic region.

What is required for random access to genomic files?

Random access requires index files: .bai for BAM, .crai for CRAM, .fai for FASTA, and .tbi or .csi for compressed VCF/BCF files. Pysam can also generate these indices programmatically.

Does Pysam use 0-based or 1-based coordinates?

Pysam follows the Python convention of 0-based, half-open coordinates for internal operations. However, it can handle 1-based strings when using the fetch() method to maintain compatibility with samtools conventions.

Can I run samtools commands through this skill?

Yes, Pysam provides a direct wrapper for samtools and bcftools, allowing you to run commands like sort, index, and view directly from your Python scripts.

Pysam Genomic Data Processing

Name: Pysam Genomic Data Processing
Author: Zehong-Wang

byZehong-Wang

0•

Data Science & ML

Processes and analyzes high-throughput sequencing data including SAM, BAM, VCF, and FASTA files using a Pythonic interface to htslib.

Pysam enables Claude to expertly handle genomic datasets within Python environments, providing the specialized logic needed for reading, manipulating, and writing standard bioinformatics formats. It offers a bridge to the htslib C-API, allowing for efficient access to alignment files (SAM/BAM/CRAM), variant files (VCF/BCF), and sequence files (FASTA/FASTQ). This skill is particularly useful for bioinformatics engineers building NGS pipelines, as it includes guidance on coordinate systems, indexing requirements, and integrated samtools/bcftools commands to ensure accurate and performant genomic data analysis.

Key Features

01Perform per-base pileup analysis and coverage calculations

02Read, write, and manipulate SAM, BAM, and CRAM alignment files

03Extract reference sequences and raw reads from FASTA and FASTQ files

04Query and filter VCF and BCF variant files with sample-level access

05Direct execution of samtools and bcftools commands within Python

060 GitHub stars

Use Cases

01Implementing custom variant annotation and filtering workflows

02Extracting specific genomic regions or variants for population genetics studies

03Developing automated NGS quality control and data processing pipelines

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos pysam

For use in Claude.ai and ChatGPT

Download Skill