Fastq to Somatic Variants (WES)
The Fastq to Somatic Variants (WES) template workflow supports analysis of WES data. 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.
It can be used to:
- Identify and annotate somatic variants and generate various QC metrics.
- Identify copy number variants if control coverage tables are provided.
- Generate control coverage tables for copy number variant detection.
Fastq to Somatic Variants (WES) can be found at:
Template Workflows | LightSpeed Workflows (
) | Fastq to Somatic Variants (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.
- Specify the workflow path The following paths can be configured:
- Analysis options Specify whether you want to
- Analyze sample Detect variants and, optionally, CNVs.
- Create CNV control Create a CNV control coverage table from a normal sample.
- Analyze sample and create CNV control Detect variants and create a CNV control coverage table.
- Detect CNVs
- No Copy number variants will not be called.
- Yes Copy number variants will be called if control coverage tables are provided in the Copy Number Variant Detection (Targeted) dialog.
- Analysis options Specify whether you want to
- 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 Reference Data Sets and defining Custom Sets.
- LightSpeed Fastq to Somatic Variants
Specify options for the LightSpeed Fastq to Somatic Variants tool:
- Reads (fastq) Press Browse to select fastq files for analysis.
- 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 Somatic variant detection for additional details.
- Lenient inversion detection When enabled, inversions with read support in only one direction at each breakpoint can be called. Enabling this option is recommended when analysing targeted data, but can increase processing time and can result in detection of more false positive inversions.
- Batch Select if fastq files from different samples are used as input, and each sample should be analyzed individually (for information about batching see Batching).
- Join lanes when batching Select to join fastq files from the same sample that were sequenced on different lanes.
- QC for Targeted Sequencing Set the Minimum coverage parameter of the QC for Targeted Sequencing tool. 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.
- Copy Number Variant Detection (Targeted), if CNV detection is enabled. Specify Controls against which the coverage pattern in your sample will be compared in order to call CNVs. If you do not supply any controls, the CNV analysis will not be carried out. Please note that if you want the CNV analysis to be done, it is important that the controls supplied are meaningful controls for the sample being analyzed. Mapping of control samples for the CNV analysis can be done by running this workflow with Analysis options set to Create CNV control or Analyze sample and create CNV control in the dialog Specify workflow path.
A meaningful control must satisfy two conditions: (1) It must have a copy number status that is meaningful to compare against. For panels with targets on the X and Y chromosomes, the control and sample should be matched for gender. (2) The control read mapping must result from the same type of processing that will be applied to the sample. For more information about CNV detection, see Copy Number Variant Detection.
- 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 Create Sample Report.
- 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.
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