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

samtools

wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.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 such as 0.x 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
# Or, you can just use the path to call samtools
/usr/loca/bin/bin/samtools -h

BCFtools

wget https://github.com/samtools/bcftools/releases/download/1.16/bcftools-1.16.tar.bz2 -O bcftools.tar.bz2
tar -xjvf bcftools.tar.bz2
cd bcftools-1.16
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/1.3.2/htslib-1.3.2.tar.bz2 -O htslib.tar.bz2
tar -xjvf htslib.tar.bz2
cd htslib-{version}
make
sudo make install

bedtools

wget https://github.com/arq5x/bedtools2/releases/download/v2.30.0/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