Outputs from Fastq to Somatic Variants (Tumor Normal) (WES)
The Fastq to Somatic Variants (Tumor Normal) (WES) template workflow produces the following outputs:
- Somatic Variants A variant track (
) with the annotated variants.
- Ignored Regions An annotation track (
) providing regions where it was not possible to
detect variants due to high complexity among the initial variants being tested.
- LightSpeed Report A report (
) summarizing details of each analysis step performed by the LightSpeed Fastq to Somatic Variants Tumor Normal 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 Somatic Variants, the Ignored Regions, the Amino Acid Track, the Target regions, the tumor Target Region Statistics Track, the tumor and normal Read Mappings as well as the Reference sequence and the Genes, mRNA and CDS tracks.
- Tumor Read Mapping A read mapping track for the tumor sample (
).
- Normal Read Mapping A read mapping track for the normal sample ().
- Amino Acid Track A track (
) providing a graphical representation of identified amino acid changes.
- Coverage Report (Normal) A report () summarizing coverage.
- Target Region Statistics Track (Normal) A track () providing coverage information per target region.
- Gene Coverage Track (Normal) A track () providing coverage information per gene.
- Coverage Report (Tumor) A report () summarizing coverage.
- Target Region Statistics Track (Tumor) A track () providing coverage information per target region.
- Gene Coverage Track (Tumor) A track () providing coverage information per gene.
The Amino Acid Track is produced by Amino Acid Changes.
The Coverage Reports, Target Region Statistics Tracks and the Gene Coverage Tracks are produced by QC for Targeted Sequencing.