WES pipelines

This pipelines is mainly designed for WES(Whole Exome Sequencing) of human, particularly the paired cancer samples.

Including two pipelines(germline & somatic)

installation

git clone https://github.com/444thLiao/WES_pipelines.git
cd WES_pipelines
pip install -r requirement.txt

others requirement need to manually install.

• bcftools
• vt
• vep
• annovar
• gatk
• samtools
• bgzip
• tabix
• trimmomatic
• picard
• pcgr

some packages are needed because of pcgr and its pipelines. So if you want to output result and directly output pcgr-like output. You need to install pcgr vep and vt.

main pipelines description

After clone this repository, please first check the setting.py file and verify the path is existed at your personal computer.

1. Download required WES data
2. Fulfil a table according to data_input.template
3. perform analysis with main.py

With below command,

python3 WES_pipelines/luigi_pipelines/main.py run -- main_entry --tab WES_pipelines/test_set/somatic/data_input.tsv --odir ~/temp/test_somatic --analysis-type somatic --workers 5 --log-path ~/temp/test_somatic/cmd_log.txt

Above code is performing pipelines used for somatic variants calling. Finally, it will output to ~/temp/test_somatic

If you want to perform germline variants calling pipelines, you just need to change the parameter of analysis-type into germline

Validate parameter of analysis-type includes:

• germline
• germline_gatk4
• somatic
• somatic_gatk4

testing data

If you only want to test the completeness of all required software, you could use below command which use testing data to validate.

python3 WES_pipelines/luigi_pipelines/main.py test-germline -o ~/temp/test_germline

If you want to test others pipelines, you could also change the parameter of test-germline into test-somatic