README.md

Tools

Steps to install GATK

1. Download gatk-4.x.x.zip file from this link

wget https://github.com/broadinstitute/gatk/releases/download/4.2.3.0/gatk-4.2.3.0.zip

2. Unzip the package on remote server

unzip gatk-4.2.3.zip

3. Set up PATH for jar files Note: change /path/to/gatk-package/ to the absolute path of your unzip folder from step 2.

export PATH="/path/to/gatk-package/":$PATH

You can also add this to your .bashrc file, so you don't need to run it everytime you want to use GATK.

echo "export PATH='/path/to/gatk-package/':$PATH >> ~/.bashrc
source ~/.bashrc

4. Test that it works

gatk info

5. Use GATK creates necessary reference files for next steps

gatk CreateSequenceDictionary R=hg38.fa O=hg38.dict

Steps to download SnpEff

1. Download latest version

wget https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip

2. Unzip file

unzip snpEff_latest_core.zip

3. Configure

export PATH=$PATH:/path/to/snpEff/

4. Download Reference Database

 java -jar ./snpEff/snpEff.jar download GRCh38.99