Create QIAseq DNA CNV Control Mapping
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) (
)
Options in the following dialogs can be configured:
- Choose where to run. If you are connected to a CLC Server via the CLC 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.
- Select Reads. Select the sequencing reads. When analyzing more than one sample at a time, check the Batch checkbox in the lower left corner of the dialog.
- Specify reference data handling. Select the relevant Reference Data Set, see Reference data management for details. For QIAseq Targeted DNA workflows, QIAseq DNA Panels hg19 will be pre-selected, whereas for QIAseq Targeted DNA Pro workflows, QIAseq DNA Pro Panels hg38 will be pre-selected.
- Configure batching. If running the workflow in Batch mode, you will be asked to define the batch units. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Running_workflows_in_batch_mode.html for details.
- Target primers. Choose the relevant target primers from the drop down list.
- Target regions. Choose the relevant target regions from the drop down list.
- Map Reads to Reference. This step is available for QIAseq DNA Pro workflows only. Here, 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.
- QC for Target Sequencing. Set the Minimum coverage parameter of the QC for Target Sequencing tool.
- Result handling. Choose if a workflow result metadata and/or log should be saved.
- Save location for new elements. Choose where to save the data, and press Finish to start the analysis.
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.
Launching using the QIAseq Panel Analysis Assistant
The workflows are also available in the QIAseq Panel Analysis Assistant under Targeted DNA and Targeted DNA Pro.
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