rmsk/README.md

ANNOVAR

This APP developed for the annotation of VCF files.

Please take care to check that the parameter hg is compatible with your reference genome reference builds version.

If the type and version of database currently used in the APP does not meet your needs, please contact the developer.

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/annovar [-f]

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

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

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