Install samtools, bcftools and htslib on linux

install-samtools-bcftools-and-htslib.md

Install samtools, bcftools, htslib, bedtools, and plink2 on linux

Install some build dependencies

sudo apt update

sudo apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev wget libncurses5-dev bzip2

Set latest version for samtools, bcftools and htslib

Substitute the number below by the latest version you can find at: https://github.com/samtools/samtools/releases Samtools, bcftools and htslib have the same latest version.

version="1.21"

samtools

wget https://github.com/samtools/samtools/releases/download/"$version"/samtools-"$version".tar.bz2 -O samtools.tar.bz2
tar -xjvf samtools.tar.bz2
cd samtools-"$version"
make
sudo make prefix=/usr/local/bin install
# if you have old version from samtools, you may remove it and create a link to new version
sudo apt remove samtools
sudo ln -s /usr/local/bin/bin/samtools /usr/bin/samtools

BCFtools

wget https://github.com/samtools/bcftools/releases/download/"$version"/bcftools-"$version".tar.bz2 -O bcftools.tar.bz2
tar -xjvf bcftools.tar.bz2
cd bcftools-"$version"
make
sudo make prefix=/usr/local/bin install
sudo ln -s /usr/local/bin/bin/bcftools /usr/bin/bcftools
# TODO add here the right address for: export BCFTOOLS_PLUGINS=/path/to/bcftools/plugins
# bcftools plugins are needed to use, for example, fill-tags, to annotate allele frequency

HTSlib

wget https://github.com/samtools/htslib/releases/download/"$version"/htslib-"$version".tar.bz2 -O htslib.tar.bz2
tar -xjvf htslib.tar.bz2
cd htslib-"$version"
make
sudo make install

bedtools

# Get the latest version at https://github.com/arq5x/bedtools2/releases/ and substitute the {version} below by it.

wget https://github.com/arq5x/bedtools2/releases/download/v{version}/bedtools.static.binary
mv bedtools.static.binary bedtools
chmod a+x bedtools
sudo mv bedtools /usr/local/bin

plink2

sudo apt-get install plink2

admixture

wget https://dalexander.github.io/admixture/binaries/admixture_linux-1.3.0.tar.gz
tar -xvzf admixture_linux-1.3.0.tar.gz

# use admixture32 to do a supervised analysis