Install bcftools liftover

Install latest bcftools

sudo apt-get remove bcftools  # In case older version done this way - ok if this fails as you don't have it
cd /tmp # Or wherever
wget https://github.com/samtools/bcftools/releases/download/1.20/bcftools-1.20.tar.bz2
bzip2 -d bcftools-1.20.tar.bz2
tar xvf bcftools-1.20.tar 
cd bcftools-1.20/
./configure
make
sudo make install

Note sudo make install can sometimes just list out the instructions you need to run rather than running them (you will need to run them).

Install liftover plugin

We need the dev version that has --write-reject (TODO: update this once it's a full release see issue )

sudo bash

mkdir -p /usr/share/bcftools/plugins
cd /usr/share/bcftools/plugins
wget https://software.broadinstitute.org/software/score/score_1.20-dev.zip
unzip score_1.20-dev.zip