VCF_Annotation

A snakemake pipeline for annotation and filtering VCF files.

List of used software tools:

• python =3.8.5
• R =4.0.3
• java =11.0.9.1
• picard =2.23.3
• vcftools =0.1.16
• bcftools =1.10.2
• plink2 =2.00a2.3LM
• tabix =1.10.2-3
• VariantAnnotation r package =1.36.0
• snakemake =5.10.0

Operating system requirements

• moreutils =0.63-1

Compilation instructions

• No compilation needed.

How to run the workflow

Method 1

Step 1: Configure workflow

Configure the workflow according to your needs via editing the file config.yaml.

Step 2: Execute workflow

Test your configuration by performing a dry-run via

$ snakemake --use-conda -n

Step 3: Execute the workflow locally via

$ snakemake --use-conda --cores $N

Method 2

Step 1: Configure workflow

Configure the workflow according to your needs via editing the file config.yaml.

Step 2: Creating an environment using environment.yaml

$ conda env create --name smake_env --file envs/environment.yaml

Step 3: Activating the environment

$ conda activate smake_env

Step 4: Running workflow

$ snakemake

To exit the environment, execute

$ conda deactivate

Expected output

• A directory called results contains output VCFs and a list of unrelated individuals.
• A directory called intermediate contains intermediate files.
• A directory called LOG contains log files.

Workflow steps (DAG)