When launching a new analysis you are asked to choose capture or amplicon kit used for sequencing of your sample. If you are uploading FASTQ files, this is important information.
Select the capture, amplicon, whole genome library preparation method or kit corresponding to your analysis. The capture/amplicon kit details will be used to calculate alignment statistics and coverage of the coding regions included in the kit.
In order to be able to give numbers like % of reads on target, we need to know what the target regions were. That's what the kit's bed file tells us. In addition, we need to know if this was an amplicon or a capture kit because we need to preprocess the reads differently. For capture kits, we need to remove PCR duplicates while for amplicons (which rely on PCR, so the dupes are normal) we don't.
We don't use these statistics measures to filter the results, instead we use it to provide quality statistics shown later in the Quality Control (QC) Report. If you do not know what kit was used to prepare the capture/amplicon library, you should choose "generic other capture kit" or "generic other amplicon kit".