Fastq to Germline Variants (WGS)
The Fastq to Germline Variants (WGS) template workflow identifies and annotates germline variants 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 Germline Variants (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 Germline Variants
Specify options for the LightSpeed Fastq to Germline 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 average quality Specify the minimum average quality of detected variants. See Germline variant detection for additional details.
- Minimum allele count Specify the minimum number of reads supporting an identified variant.
- 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.
- 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