The Preparing Raw Data ready-to-use workflows are universal and can be used for all applications; Whole Genome Sequencing, Exome Sequencing, and Targeted Amplicon Sequencing. But many whole genome sequencing, exome sequencing using capture technology, and targeted amplicon sequencing strategies produce overlapping reads. Downstream stages of the Biomedical Genomics Workbench (e.g. variant calling) take the frequencies of observed alleles into consideration as well as the forward-reverse strand balance. When merging overlapping reads these two parameters will be affected: 1) the frequency of observed alleles in overlapping regions will be corrected (a variant found both on the forward and the reverse read of the same fragment should only be counted once), and 2) in the merged fragments the information on forward-reverse strand origin has become meaningless. These effects have to be taken into consideration when filtering variants on these statistics. As the forward-reverse strand balance statistic is used as a variant filter (i.e. the Read direction filter), we recommend using the "Prepare Overlapping Raw Data" workflow on targeted amplicon sequencing data with overlapping read sequencing strategy, whereas we recommend the "Prepare Raw Data" workflow for other sequencing protocols (e.g. whole genome sequencing, whole exome-sequencing, also if making use of overlapping read sequencing).