pysam - Genomic Data File Processing
Read/write genomic files including SAM/BAM alignments, VCF variants, and FASTA/FASTQ sequences with Python interface to htslib.
Tags
Updated: 2026-06-15Capabilities
Typical Inputs
Typical Outputs
What this skill does
- read SAM/BAM/CRAM files
- write SAM/BAM/CRAM files
- read VCF/BCF files
- write VCF/BCF files
- read FASTA/FASTQ files
- write FASTA/FASTQ files
- extract genomic sequences
- calculate coverage statistics
- perform pileup analysis
- query indexed files
- filter alignments
- filter variants
- filter reads
Inputs
- SAM/BAM/CRAM files
- VCF/BCF files
- FASTA/FASTQ files
- BAM index
- CRAM index
- FASTA index
- tabix index
- CSI index
Outputs
- SAM/BAM/CRAM files
- VCF/BCF files
- FASTA/FASTQ files
- coverage statistics
- extracted sequences
- filtered alignments
- filtered variants
Requirements
- Python 3.x
- pysam package
- index files for random access