pysam

Read and write SAM/BAM/CRAM alignments and VCF/BCF variants using pysam.

52|6|Updated Nov 24, 2025

Search Tags:#VCF #htslib #pysam #FASTA #BAM

Ready to run

npx skills add https://github.com/ovachiever/droid-tings --skill pysam

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: pysam
Source: https://github.com/ovachiever/droid-tings/tree/main/skills/pysam
Command: npx skills add https://github.com/ovachiever/droid-tings --skill pysam

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pysam, and includes references (resource) components.

What problem does it solve?

Pysam provides Python bindings to htslib for efficient reading, writing, and querying of SAM/BAM/CRAM, VCF/BCF, FASTA/FASTQ, plus indexing and pileup analyses, enabling robust NGS pipelines.

Core Features & Use Cases

Read/write BAM/CRAM/SAM: Access alignments, fetch regions, and compute coverage.
Variant handling: Query and process VCF/BCF data; count and annotate variants.
Sequence access: Random access to indexed reference sequences via FastaFile.
Workflows: End-to-end pipelines combining alignment, variant, and sequence data.

Quick Start

Open a BAM file, fetch reads in a region, and fetch a FASTA sequence from the reference.

Frequently Asked Questions about pysam

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I read and filter alignments from a BAM file by genomic region?▼

BAM files store sequencing alignments; pysam's AlignmentFile class enables random-access region queries using 0-based half-open coordinates or 1-based region strings, returning filtered reads for alignment handling and coverage analysis in NGS pipelines.

Can I query VCF variants and extract specific genomic regions programmatically?▼

VCF files store variant calls; pysam's VariantFile provides tabix-indexed access to variants by region, enabling variant counting, annotation, and format conversion (VCF to BCF) within NGS analysis workflows.

What's the best way to access reference sequences and calculate per-base coverage?▼

Pysam's FastaFile enables random-access lookups of indexed reference sequences, while pileup methods compute per-base coverage and quality metrics directly from alignments, satisfying reference-aware QC and region extraction tasks.

How do I build an end-to-end NGS pipeline combining alignment, variant, and sequence data?▼

Pysam integrates SAM/BAM/CRAM reading, VCF/BCF variant processing, and FASTA/FASTQ sequence access into unified workflows; coordinate-aware queries across formats enable alignment-to-variant linkage and comprehensive data processing.

Does pysam support CRAM format and tabix-indexed random access for large datasets?▼

Pysam wraps htslib, supporting CRAM compression for efficient storage and tabix indexing for rapid region retrieval across BAM, VCF, and FASTA formats, scaling to large-scale sequencing datasets.

What format conversions and quality checks can I perform on sequencing data?▼

Pysam enables SAM↔BAM↔CRAM conversion, VCF↔BCF translation, and FASTQ validation; pileup-based coverage analysis and per-base metrics support quality control and alignment assessment in production NGS pipelines.