Create QIAseq DNA CNV (Pro) Control Mapping template workflows generate mappings suitable for use as baseline, control mappings for the CNV detection step of the Identify QIAseq DNA (Pro) Variants template workflows (see The Identify QIAseq DNA Variants template workflows). We recommend a minimum of 3 control samples be used for creating control mappings.
The Create QIAseq DNA CNV Control Mapping workflows can be found at:
Template Workflows | Biomedical Workflows () | QIAseq Sample Analysis () | QIAseq DNA workflows () | Create QIAseq DNA CNV Control Mapping (Illumina/Ion Torrent) ()
The Create QIAseq DNA Pro CNV Control Mapping workflows can be found at:
Template Workflows | Biomedical Workflows () | QIAseq Sample Analysis () | QIAseq DNA workflows () | Create QIAseq DNA Pro CNV Control Mapping (Illumina/Ion Torrent) ()
These workflows can also be launched from the Analyze QIAseq Samples guide, which is described in The Analyze QIAseq Samples guide. They are available in the drop down menus under each panel analysis listed under either the Targeted DNA or the Targeted DNA Pro tab.
If you are connected to a CLC Server via your Workbench, you will be asked where you would like to run the analysis. We recommend that you run the analysis on a CLC Server when possible.
In the Select reads dialog, specify the sequencing reads to be analyzed.
The following dialog helps you set up the relevant Reference Data Set. If you have not downloaded the Reference Data Set yet, the dialog will suggest the relevant data set and offer the opportunity to download it using the Download to Workbench button.
We recommend that the default QIAseq reference data is selected for use, both when generating control mappings and when analyzing cases using the Identify QIAseq DNA Variants template workflows.
In the next dialog, select the primer track specific to the QIAseq DNA Panel used to generate the sequenced reads. The primer files are specific to the bundles chosen when selecting the reference data.
For QIAseq Pro workflows only: In the Map Reads to Reference dialog, it is possible to configure masking. A custom masking track can be used, but by default, the masking track is set to GenomeReferenceConsortium_masking_hg38_no_alt_analysis_set, containing the regions defined by the Genome Reference Consortium, which serve primarily to remove false duplications, including one affecting the gene U2AF1. Changing the masking mode from "No masking" to "Exclude annotated" excludes these regions.
Note that reads that span the origin of the MT chromosome are not trimmed by the Trim Primers of Mapped Reads tool when running the Identify QIAseq DNA Variants template workflows on data from the DHS-105Z panel.