Fastq to Somatic Variants (Tumor Normal) (WES)
The Fastq to Somatic Variants (Tumor Normal) (WES) template workflow identifies and annotates somatic variants and generates various QC metrics. It is intended for analysis of data generated with target enrichment, including whole exome sequencing (WES) data, and therefore requires target regions to be provided.
Fastq to Somatic Variants (Tumor Normal) (WES) can be found at:
Template Workflows | LightSpeed Workflows (
) | Fastq to Somatic Variants (Tumor Normal) (WES) (
)
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.
- Select Target regions Specify target regions for analysis.
- 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 Normaltool:
- 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.
- QC for Targeted Sequencing (Normal) Set the Minimum coverage parameter of the QC for Targeted Sequencing tool for the normal read mapping. Using default settings, samples where 90 percent of target region positions do not meet this threshold will be flagged in the sample report generated by the workflow.
- QC for Targeted Sequencing (Tumor) Set the Minimum coverage parameter of the QC for Targeted Sequencing tool for the tumor read mapping. Using default settings, samples where 90 percent of target region positions do not meet this threshold will be flagged in the sample report generated by the workflow.
- 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.
Note that to be able to add information from both the normal and the tumor reports from QC for Targeted Sequencing to the sample report, the reports are retyped using the Modify Report Type tool. To select additional summary items for the two reports, the following steps are needed: After pressing Add..., select the QC for Targeted Sequencing report type. Then check "Apply to custom report type" and write either "QC for Targeted Sequencing (Normal)" or "QC for Targeted Sequencing (Tumor)" as relevant before selecting summary items.
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