pysam
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
This page mirrors an upstream repository entry. It does not mean the skill is already part of the SCI Skills curated catalog.
- Raw path
- scientific-skills/pysam
- Allowed tools
- -
- Repository version
- 2.31.0
- Synced at
- March 27, 2026
About this skill
About this skill
Pysam is a Python module for reading, manipulating, and writing genomic datasets. Read/write SAM/BAM/CRAM alignment files, VCF/BCF variant files, and FASTA/FASTQ sequences with a Pythonic interface to htslib. Query tabix-indexed files, perform pileup analysis for coverage, and execute samtools/bcftools commands.
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