Outputs from Twist CGP Fastq to Somatic Variants
The Twist CGP Fastq to Somatic Variants 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:
- Variants A variant track (
) with the annotated variants.
- LightSpeed Report A report (
) summarizing details of each analysis step performed by the LightSpeed Fastq to Somatic Variants tool.
- Read Mapping A read mapping track (
) with the mapped reads.
- Coverage Report A report () summarizing coverage.
- Per Region Statistics Track A track (
) providing coverage information per target region. The Coverage Report and the Per Region Statistics Track are produced by QC for Targeted Sequencing.
- Amino Acid Track A track (
) providing a graphical representation of identified amino acid changes. The Amino Acid Track is produced by Amino Acid Changes.
- Genome Browser View A track list (
) containing the Reference sequence, the Per Region Statistics Track, the Read Mapping, Variants, Gene-level CNVs and Fusion Genes (if detection enabled), the Genes, mRNA, CDS and the Amino Acid Track.
- 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.
- Additionally, if CNV detection is enabled:
- CNV Results Report A report () providing an overview of identified CNVs.
- 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.
- Target-level CNV Track An annotation track () providing CNV results per target.
The results are produced by Copy Number Variant Detection (Targeted), see Copy Number Variant Detection for details. CNV results are reported for only a subset of the full set of targeted genes.
- CNV Results Report A report (
- Additionally, if fusion detection is enabled:
- Fusion report (): A report summarizing the identified fusions.
- Fusion Unaligned Ends (): The unaligned ends mapped to the reference genome.
- Fusion Genes (): A track containing the breakpoints on the reference genome of detected fusions that have passed all relevant filters.
The results are produced by Detect Fusion Genes from DNA, see Detect Fusion Genes from DNA for details.
- Fusion report (
- Additionally, if MSI detection is enabled:
- MSI report () A report containing the MSI status of the sample and the stability of the individual loci.
- MSI Loci Track () An annotation track containing the MSI loci annotated with predicted stability.
The results are produced by Detect MSI Status, see Detect MSI Status for details.
- MSI report (
- Additionally, if TMB calculation is enabled:
- TMB report () A report containing the TMB score and confidence values.
- TMB Somatic Variants () Filtered variants that are included in the TMB score calculation.
The results are produced by Calculate TMB Score (LightSpeed), see Calculate TMB Score (LightSpeed) for details.
- TMB report (
- Additionally, if Prepare for QCI Interpret Upload is enabled:
- QCI Interpret report () A report containing the sample analysis results in a form that allows for later upload to QCI Interpret.
The report is produced by Prepare QCI Interpret Upload, see Prepare QCI Interpret Upload for details.
- QCI Interpret report (
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.