The GATK-pipeline is build for variant calling on NGS data (preferably Illumina data).
It is based on 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 <samplename>.
The pipeline accepts ```.fastq & .bam``` files as input.