Outputs from Fastq to Germline Variants (WES)
The Fastq to Germline Variants (WES) template workflow can produce a number of outputs depending on the settings that are chosen in the Specify workflow path wizard step.Sample analysis outputs that are available when Analysis options is set to Analyze sample or Analyze sample and create CNV control:
- Germline Variants A variant track (
) with the annotated variants.
- Inversions An annotation track (
) providing the called inversions.
- LightSpeed Report A report (
) summarizing details of each analysis step performed by the LightSpeed Fastq to Germline Variants tool.
- Sample Report A report () that contains compiled QC metrics from other reports and provides an overview of a given sample. The report contains a quality control section reflecting the summary items specified in the Create Sample Report wizard step.
- Genome Browser View A track list (
) containing the Germline Variants, the Amino Acid Track, the Target regions, the Target Region Statistics Track, the Gene-level CNV Track, the Read Mapping as well as the Reference sequence and the Genes, mRNA and CDS tracks.
- Read Mapping A read mapping track (
).
- Amino Acid Track A track (
) providing a graphical representation of identified amino acid changes.
- Coverage Report A report () summarizing coverage.
- Target Region Statistics Track A track () providing coverage information per target region.
- Gene Coverage Track A track () providing coverage information per gene.
CNV control output that is available when Analysis options is set to Create CNV Control or Analyze sample and create CNV control:
- Coverage table (
) Contains the coverage for every target region position and can be used as control in Copy Number Variant Detection (Targeted). See Coverage table for details.
Copy number variant detection results that are available when Detect CNVs is set to Yes:
- CNV Results Report A report () providing an overview of identified CNVs.
- Target-level CNV Track An annotation track () providing CNV results per target.
- Gene-level CNV Track An annotation track () providing CNV results per gene.
- Region-level CNV Track An annotation track () providing CNV results per region, where regions are formed from adjacent targets with similar CNV states.
The Amino Acid Track is produced by Amino Acid Changes.
The CNV Results Report, and the Target, Gene and Region-level CNV Tracks are produced by Copy Number Variant Detection (Targeted), see Copy Number Variant Detection.
The Coverage Report, Target Region Statistics Track and the Gene Coverage Track are produced by QC for Targeted Sequencing.