MOLGENIS Pipelines

Updated an hour ago

MOLGENIS pipelines


This repository contains the following pipelines:

  • Alignment
  • Imputation
  • GWAS
  • RNA-seq (Experimental)

In addition it contains protocols that may be re-used between different (versions of a) pipeline(s).

How to get started

Below we explain (step 1) how to download and deploy Molgenis Compute. This distribution already contains several pipelines/protocols/parameter files which you can use 'out-of-the-box' to align and impute your NGS data. Next, we explain (step 2) how you can download even more pipelines and protocols by cloning this repo.

For a 'walkthrough' tutorial on Molgenis Compute, please visit

Step 1: download Molgenis Compute

Download the latest MOLGENIS Compute from

Currently (March 2013)

create dir

mkdir mycompute cd mycompute


wget unzip molgenis_compute-\.zip mv molgenis_compute-\/* .



Step 2: clone this repo

For read/write access:

git clone

Alternatively to only download the pipelines use:

wget unzip master

Table of Contents