YaqingLiu/VEP: VEP (Variant Effect Predictor) predicts the functional effects of genomic variants. The annotated VCF will be converted into MAF based on vcf2maf.

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

YaqingLiu 4e2f03dfe4 Fixbug: conflicting output names		vor 4 Jahren
tasks	Fixbug: conflicting output names	vor 4 Jahren
LICENSE.md	vcf2maf	vor 4 Jahren
README.md	Alter README	vor 4 Jahren
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workflow.wdl	Alter: add output vcf	vor 4 Jahren

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

.maf