SAMtools

Samtools Toggle navigation Samtools Home Download Downloads Development Workflows FASTQ to BAM / CRAM WGS/WES Mapping to Variant Calls Filtering of VCF Files Using CRAM within Samtools Documentation Man Pages HowTos Specifications Duplicate Marking Zlib Benchmarks CRAM Benchmarks Reference Sequences Publications Support HTSlib issues BCFtools issues Samtools issues General help Samtools Samtools is a suite of programs for interacting with high-throughput sequencing data.

It consists of three separate repositories: Samtools Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format BCFtools Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants HTSlib A C library for reading/writing high-throughput sequencing data Samtools and BCFtools both use HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.

Download Source code releases can be downloaded from GitHub or Sourceforge :  Source release details Workflows We have described some standard workflows using Samtools: FASTQ to BAM / CRAM WGS/WES Mapping to Variant Calls Filtering of VCF Files Using CRAM within Samtools Documentation Manuals HowTos Specifications Duplicate Marking Zlib Benchmarks CRAM Benchmarks Reference Sequences Publications Support HTSlib issues BCFtools issues Samtools issues General help Copyright © 2025 Genome