WES pipeline & analysis tools

Maintainer: Li Hsin Chang Contact: cc1296@ym.edu.tw

VGHTPE Ihlee lab dockerized WES pipeline backup

Automated script

You can use my python script to build up the whole envrionment though the script may not work on your workstation. The script will set up docker, docker-compose and asking whether download GATK resource bundle and ANNOVAR references or not. Download these DBs will be a long proccess and I did not write an auto reconnect mechanism so I suggest you can download GATK resource buldle via filezella or other FTP clients.

Requirement: Python3 & distro module

git clone https://github.com/onlelonely/WES.git
cd WES
python install.py

or you can dou it manually

Getting started

First of all, you need to install Docker & docker compose.

Full instructions at https://docs.docker.com/.

For CentOS

sudo yum-config-manager \
    --add-repo \
    https://download.docker.com/linux/centos/docker-ce.repo
sudo yum install docker-ce
sudo yum -y install epel-release 
sudo yum -y install python-pip  
sudo pip install docker-compose 
sudo yum -y upgrade python* 

For Ubuntu

curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo apt-key add -
sudo add-apt-repository "deb [arch=amd64] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable"
sudo apt-get update
sudo apt-get install -y docker-ce

In order to use docker as non-root user, you need to do the following:

sudo addgroup docker
sudo usermod -aG docker $USER

To verify the installation, you can

docker run --rm hello-world

and you'll get

Hello from Docker! This message shows that your installation appears to be working correctly.

To generate this message, Docker took the following steps:

1. The Docker client contacted the Docker daemon.
2. The Docker daemon pulled the "hello-world" image from the Docker Hub. (amd64)
3. The Docker daemon created a new container from that image which runs the executable that produces the output you are currently reading.
4. The Docker daemon streamed that output to the Docker client, which sent it to your terminal.

To try something more ambitious, you can run an Ubuntu container with: $ docker run -it ubuntu bash

Share images, automate workflows, and more with a free Docker ID: https://hub.docker.com/

For more examples and ideas, visit: https://docs.docker.com/engine/userguide/

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Set up reference DBs & build docker images

You can download GATK resource bundle via FTP client.

HOST:ftp.broadinstitute.org
USER:gsapubftp-anonymous
PASSWORD:

And you can download ANNOVAR references via annotate_variation.pl

perl annotate_variation.pl -buildver {hg version} -downdb -webfrom annovar {db name} {path}

For example, the DBs I use are hg38 version and store in ref/humandb folder

perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar refgene ref/humandb
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar ensGene ref/humandb
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar 1000g2015aug ref/humandb
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar avsnp150 ref/humandb
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar dbnsfp33a ref/humandb
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar gnomad_genome ref/humandb
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar gnomad_exome ref/humandb
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar clinvar_20180603 ref/humandb
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar dbscsnv11 ref/humandb
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar intervar_20180118 ref/humandb
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar esp6500siv2_all ref/humandb
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar exac03 ref/humandb
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar mcap ref/humandb
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar revel ref/humandb