Pysam — Genomic File Toolkit

Pysam — Genomic File Toolkit

Overview

Pysam provides a Pythonic interface to htslib for reading, manipulating, and writing genomic data files. It handles SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences with efficient region-based random access. Also exposes samtools and bcftools as callable Python functions.

When to Use

• Reading and querying BAM/CRAM alignment files (region extraction, read filtering)
• Analyzing VCF/BCF variant files (genotype access, variant filtering, annotation)
• Extracting reference sequences from indexed FASTA files
• Calculating per-base coverage and pileup statistics
• Building custom bioinformatics pipelines that combine alignment + variant + sequence data
• Quality control of NGS data (mapping quality, flag filtering, coverage)
• For alignment from FASTQ (read mapping), use STAR, BWA, or minimap2 instead
• For variant calling from BAM, use GATK or DeepVariant instead

Prerequisites

pip install pysam

Note: Requires htslib C library (bundled with pip install on most platforms). On some Linux systems, may need libhts-dev or equivalent. Index files (.bai, .tbi, .fai) required for random access — create with pysam.index(), pysam.tabix_index(), or pysam.faidx().

Pre-flight Interview

Settle these with the user before writing any analysis code.

decisions:
  - id: D1
    param: mappingQualityFloor
    kind: required
    source: user
    ask: "Below what mapping confidence should reads be ignored when piling up or counting?"
    default: "0 - no filter"

  - id: D2
    param: baseQualityFloor