Outputs from Fastq to Annotated Somatic Variants (Tumor Normal) with Coverage Analysis
The Fastq to Annotated Somatic Variants (Tumor Normal) with Coverage Analysis template workflow produces the following outputs:
- Somatic Variants The 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 summarizing the most important metrics from the LightSpeed Report and the Coverage Reports. 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.
- Read Mapping A read mapping track (
).
- 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 (http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Amino_Acid_Changes.html).
The Coverage Reports, Target Region Statistics Tracks and the Gene Coverage Tracks are produced by QC for Targeted Sequencing (http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=QC_Targeted_Sequencing.html).