run_missingGATK_steps

#We need some additional files for processing steps
aws s3 cp s3://kite.sb/references/gatk_resources/af-only-gnomad.hg38.PASS.vcf.gz /home/ubuntu/gatk_out
aws s3 cp s3://kite.sb/references/gatk_resources/af-only-gnomad.hg38.PASS.vcf.gz.tbi /home/ubuntu/gatk_out

#we need to install vp to run some normalization
git clone https://github.com/atks/vt.git
cd vt
git submodule update --init --recursive
make

~/gatk_out/vt/vt normalize /home/ubuntu/gatk_out/germline_jointcalls_filtered.vcf.gz -o germline_jointcalls_filtered_normalized.vcf.gz -r reference/Homo_sapiens_assembly38.fasta


git clone https://github.com/Ensembl/ensembl-vep.git
cd ensembl-vep/
sudo apt-get install libdbi-perl
perl INSTALL.pl -a p -g list
perl -MModule::Build -le 'print $Module::Build::VERSION'
perl INSTALL.pl
sudo apt-get install -y libmodule-build-perl
sudo apt-get install -y libdbd-mysql-perl

##
cd /home/ubuntu/.vep

#I moved the files I was going to work with to that folder
mv /home/ubuntu/gatk_out/germline_jointcalls_filtered.vcf.gz /home/ubuntu/.vep

#Then ran vep with the default
~/ensembl-vep/vep -i germline_jointcalls_filtered.vcf.gz --cache