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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
   * Publications
 * Support
   * Mailing Lists
   * HTSlib issues
   * BCFtools issues
   * Samtools issues


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
 * Publications


SUPPORT

 * Mailing Lists
 * HTSlib issues
 * BCFtools issues
 * Samtools issues

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