Outputs from Fastq to Annotated Somatic Variants with Coverage Analysis
The Fastq to Annotated Somatic Variants with Coverage Analysis template workflow produces the following outputs:
- Somatic Variants The variant track (
) with the annotated variants.
- Inversions An annotation track (
) providing the called inversions.
- 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 tool.
- Sample Report A report () summarizing the most important metrics from the LightSpeed Report and the Coverage Report. 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 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.
- 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.
- 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.
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 CNV Results Report, and the Target, Gene and Region-level CNV Tracks are produced by Copy Number Variant Detection (CNVs) (http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Copy_Number_Variant_Detection.html).
The Coverage Report, Target Region Statistics Track and the Gene Coverage Track are produced by QC for Targeted Sequencing (http://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=QC_Targeted_Sequencing.html).