Use of target regions BED files with a copied or edited analysis
When you copy an analysis workflow in Ion Reporter™ Software, in most cases, the parameters used for the Torrent Variant Caller (TVC) software component are the same as those contained in the analysis workflow which was copied. However, in a few cases, if you select a new target regions BED file that was imported from AmpliSeq.com, the TVC parameters settings are based on the values that are contained in the imported files. Panels that can include TVC parameters are Ready-to-Use Ion AmpliSeq™ panels, and custom panels and community panels imported from AmpliSeq.com.
In these cases, when you copy an analysis workflow from a customized workflow, and then change the target regions BED file, the parameter settings depend on how the target regions BED file is created.
The choices and information about the parameter settings are as follows.
|
Choice |
Information about TVC parameter settings |
|---|---|
| Target regions BED file associated with a predefined analysis workflow | TVC parameters and the values associated with the BED file (if any) are used to update the TVC parameters of the edited workflow. |
| Target regions BED file from AmpliSeq.com | If a new target region bed file that was imported from AmpliSeq.com is selected, the TVC parameters can be set based on the values that are contained in the imported files. |
| All other target regions BED files | Parameters that are associated with the copied analysis workflow are used to update the parameters of the analysis workflow that is edited (with the selection of a target regions BED file). |
To use a new target regions BED file, copy the workflow, then adjust the parameters, instead of editing a workflow. That is, use instead of to ensure that the correct TVC parameters are used.