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Nov 27, 2018.

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SAMtools and BCFtools are distributed as individual packages.The code uses HTSlib internally, but these source packages contain their owncopies of htslib so they can be built independently.

HTSlib is also distributed as a separate package which can be installedif you are writing your own programs against the HTSlib API.HTSlib also provides the bgzip, htsfile, and tabix utilities,so you may also want to build and install HTSlib to get these utilities,or see the additional instructions in INSTALL to install them from asamtools or bcftools source package.

Download current source releases: samtools-1.11 bcftools-1.11 htslib-1.11

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See also release notes forsamtools,bcftools,and htslib.

New releases are announced on the samtools mailing lists and by @htslibon Twitter.Previous releases are available from thesamtools GitHub organisation(see samtools,bcftools,or htslib releases)or from thesamtools Sourceforge project.

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Building and installing

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Building each desired package from source is very simple:

See INSTALL in each of the source directories for further details.

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The executable programs will be installed to a bin subdirectory underyour specified prefix, so you may wish to add this directory to your $PATH:

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Historical SAMtools/BCFtools 0.1.x releases

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Prior to the introduction of HTSlib, SAMtools and BCFtools were distributedin a single samtools-0.1.x package.These old versions remain available from the Sourceforge samtools project.