Fastq to Somatic Variants (Tumor Normal) (WGS)
The Fastq to Somatic Variants (Tumor Normal) (WGS) template workflow identifies and annotates somatic variants from tumor normal reads and generates various QC metrics. It is intended for analysis of whole genome sequencing (WGS) data.
The workflow can be found at:
Template Workflows | LightSpeed Workflows (
) | Fastq to Somatic Variants (Tumor Normal) (WGS) (
)
Options in the following dialogs can be configured:
- Choose where to run 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.
- Specify reference data handling Select a 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. If none of the available reference data sets are appropriate, custom reference data sets can be created, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Reference_Data_Sets_defining_Custom_Sets.html.
- LightSpeed Fastq to Somatic Variants Tumor Normal
Specify options for the LightSpeed Fastq to Somatic Variants Tumor Normal tool:
- Tumor reads (fastq) Press Browse to select fastq files for the tumor reads.
- Normal reads (fastq) Press Browse to select fastq files for the normal reads.
- Masking mode To enable reference masking when mapping reads, set this option and select a masking track.
- Masking track Provide a masking track for the chosen reference genome if reference masking has been enabled.
- Discard duplicate mapped reads Duplicate mapped reads are per default replaced with a consensus read. Untick if duplicate mapped reads should be retained. See Deduplication for additional details.
- Minimum frequency (%) Specify the minimum variant allelle frequency for detected variants.
- Minimum average quality Specify the minimum average quality of detected variants. See Tumor normal variant detection for additional details.
- Create Sample Report Select relevant summary items and specify thresholds for quality control. Summary items, thresholds and an indication of whether specified thresholds were met, will be shown in the quality control section of the sample report. The default summary items are appropriate for many data sets, but may need to be adjusted. For additional information, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Create_Sample_Report.html.
- 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.
Subsections