| 7 | | Based on Broad pipeline. |
| 8 | | |
| 9 | | To perform the analysis as fast and good as possible the pipeline has been divided into several small processes. These processes are all numbered and can be found in figure 1 & 2 in the appendix. The processes including commands, input and output files are described below, starting with pre-alignment. |
| | 7 | Based on [http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit Broad GATK pipeline]. |
| | 8 | |
| | 9 | To perform the analysis as fast and good as possible the pipeline has been divided into several small processes. These processes are all numbered and can be found below, including commands, input and output files starting with pre-alignment and ending with variation calling & filtering. |
