VEP/README.md

VEP (Variant Effect Predictor)

VEP predicts the functional effects of genomic variants. The annotated VCF will be converted into MAF based on vcf2maf.

Getting Started

We recommend using choppy system and Aliyun OSS service. The command will look like this:

# Activate the choppy environment
$ open-choppy-env

# Install the APP
$ choppy install YaqingLiu/VEP [-f]

# List the parameters
$ choppy samples YaqingLiu/VEP-latest [--no-default]

# Submit you task with the `samples.csv file` and `project name`
$ choppy batch YaqingLiu/VEP-latest samples.csv -p Project [-l project:Label]

# Query the status of all tasks in the project
$ choppy query -L project:Label | grep "status"

Output

1. INPUT.vcf
2. maf
3. BND.VEP.txt