pysam - Genomic file toolkit for NGS data
Read and write genomic files including SAM/BAM/CRAM alignments, VCF/BCF variants, and FASTA/FASTQ sequences
Tags
Updated: 2026-06-15Capabilities
Typical Inputs
Typical Outputs
What this skill does
- read alignment files
- read variant files
- read sequence files
- write alignment files
- write variant files
- write sequence files
- extract genomic regions
- query variant records
- filter alignments
- filter variants
- calculate coverage
- count reads
- validate variants
- annotate variants
- create file indexes
Inputs
- SAM/BAM/CRAM files
- VCF/BCF files
- FASTA/FASTQ files
- genomic coordinates
Outputs
- BAM/SAM/CRAM files
- VCF/BCF files
- FASTA/FASTQ files
- coverage statistics
- variant annotations
- read counts
Requirements
- Python environment
- htslib library
- file read/write permissions
- BAM/CRAM index files (.bai/.crai)
- FASTA index files (.fai)
- VCF/BCF index files (.tbi/.csi)