Identify QIAseq xHYB Germline Variants including Mitochondrial

The Identify QIAseq xHYB Germline Variants including Mitochondrial template workflow calls germline variants in QIAseq xHYB panel target regions, as described in Identify QIAseq xHYB Germline Variants and in target regions associated with a mitochondrial spike-in.

It can be found at:

        Template Workflows | Biomedical Workflows (Image biomedical_twf_folder_open_16_n_p) | QIAseq Sample Analysis (Image qiaseqrna_folder_closed_16_n_p) | QIAseq DNA workflows (Image qiaseq_workflows_folder_closed_16_n_p) | Identify QIAseq xHYB Germline Variants including Mitochondrial (Image qiaseq_germline9)

This workflow can also be launched from the Analyze QIAseq Samples guide, which is described in The Analyze QIAseq Samples guide. It is available under the xHYB Human tab.

Mitochondrial variant calling is performed using the Low Frequency Variant Detection tool. The parameters for this can be set in the relevant wizard step when launching the workflow (figure 14.6). For a description of the different parameters that can be adjusted, see http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Low_Frequency_Variant_Detection.html. If you click on "Locked Settings", you will be able to see all parameters used for variant detection in the template workflow. Resulting variants are filtered using a different filtering cascade compared to variants obtained from the Fixed Ploidy Variant Detection tool. The settings of the filtering cascade are locked by default.

Image xhyb_germline_lfvd
Figure 14.6: Specify the parameters for the Low Frequency Variant Detection tool.

Please note that copy number variation analysis is restricted to QIAseq xHYB panel target regions and will therefore not be performed for mitochondrial target regions.

The following output files are created separately for mitochondrial data: