vep-annotation-nf

Demo pipeline for annotating variants in .vcf files using Variant Effect Predictor (VEP).

Installation

Clone this repo:

git clone https://github.com/stevekm/vep-annotation-nf.git
cd vep-annotation-nf

Nextflow

Install nextflow in the current directory with the command in the Makefile.

make install

VEP: Docker

To install VEP using Docker, run the Makefile command in the container directory.

cd container
make docker-build

VEP: conda

To install VEP using conda (for NYULMC Big Purple HPC), instead run the conda-install recipe from the Makefile in the parent repo directory.

make conda-install

Reference Files

VEP reference files will be downloaded automatically by the pipeline. However the hg19 genome fasta, fasta.fai, and fasta.dict files must also be obtained (not included; try these). On NYULMC Big Purple, all required files are already cached and no download should be needed. On other systems, the command line arguments specifying the genome fasta files should be provided separately when running, or place the files genome.fa, genome.fa.fai, and genome.dict inside the included ref directory.

Run

The Makefile includes shortcuts to help run the pipeline easier on NYULMC Big Purple HPC.

make run

The command can also be used to run on other systems, it will simply invoke the command:

./nextflow run main.nf -resume

Nextflow params values can be passed on the command line:

./nextflow run main.nf -resume --ref_fa /path/to/genome.fa --ref_fai /path/to/genome.fa.fai --ref_dict /path/to/genome.dict

Output

Output files will be collected in the output directory.

Software

Tested on RHEL 7, macOS 10.12

• Nextflow (Java 8+)

• bash

• GNU make

• Python 2.7+