The GATK-pipeline is build for variant calling on NGS data (preferably Illumina data).
It uses the <ahref="https://www.broadinstitute.org/gatk/guide/best-practices"target="_blank">best practices</a>) of GATK in terms of there approach to variant calling.
The pipeline accepts ```.fastq & .bam``` files as input.
@@ -60,13 +60,8 @@ This can be used in the root of the config or within the flexiprep, within flexi
A dual licensing model is applied. The source code within this project is freely available for non-commercial use under an AGPL license; For commercial users or users who do not want to follow the AGPL license, please contact sasc@lumc.nl to purchase a separate license.
# Invocation
# Example
Note that one should first create the appropriate [configs](../config.md).