Output from Analyze QIAseq Hybrid Capture DNA Somatic (with UMI)
The following outputs are generated:
- Genome browser view (
): Collection of output tracks, allowing multiple data types at the same genomic position to be viewed simultaneously. Note that not all output tracks are necessarily in the browser. Tracks can be added and removed from the browser.
- Sample report (
): Sample report containing essential information from all reports produced by the workflow.
- Variants (
): Detected variants.
- Additionally, if detecting fusions:
- Fusion genes (
): Breakpoints on the reference genome of detected fusions that have passed all relevant filters.
- Fusion genes (
- Additionally, if detecting CNVs:
- Gene-level CNV track (): Genes affected by CNVs.
- Gene-level CNV track (
- Additionally, if 'Analysis options' in the Specify workflow path wizard step is set to create a CNV control:
- Coverage table (
): Coverage for every target region position. Can be used as control in Copy Number Variant Detection (Targeted).
- Coverage table (
- Additionally, if preparing for QCI Interpret:
- QCI Interpret report (): Report prepared for uploading to QCI Interpret and QCI Interpret Translational.
- QCI Interpret report (
- QC & Reports folder:
- Coverage report raw reads (
): Summarizes coverage statistics for mapped raw reads in target regions. The report is based on extended target regions and provides QC for on-target mapping specificity.
- Coverage report UMI reads (): Summarizes coverage statistics for mapped UMI reads in target regions. The report assesses whether the sample has sufficient coverage for variant detection.
- Mapping report (): Summarizes the performed read mapping.
- QC report (): Summarizes and visualizes various statistics of the input reads.
- Remove and annotate UMI report (): Summarizes the identified UMIs.
- Remove ligation artifacts report (): Summarizes ligation artifacts found in and removed from the read mapping.
- Structural variants report (): Summarizes the number and different types of identified structural variants.
- Trim reads report (): Summarizes the performed read trimming
- UMI groups report (): Summarizes the UMI groups.
- UMI reads report (): Summarizes the UMI reads.
- Additionally, if detecting CNVs:
- CNV results report (): Summarizes the identified CNVs.
- CNV results report (
- Additionally, if detecting fusions:
- Fusion report (): Summarizes the identified fusions.
- Fusion report (
- Additionally, if detecting MSI:
- MSI report (): Contains the MSI Status and the stability of the individual loci.
- MSI report (
- Additionally, if calculating TMB:
- TMB report (): Contains the TMB score and confidence values.
- TMB report (
- Coverage report raw reads (
- Tracks folder:
- Amino acid changes (
): Amino acid changes introduced by the detected variants.
- ID SNP variants (). A track showing the detected variants at ID SNP positions, which can be used to assess whether samples are from the same patient.
- Indels indirect evidence (): Filtered indels.
- Mapped UMI reads (
): UMI reads mapped to the reference genome.
- Per-region statistics track (): Coverage statistics for each target region.
- Additionally, if detecting MSI:
- MSI loci track (): MSI loci annotated with microsattelite stability.
- MSI loci track (
- Additionally, if detecting CNVs:
- Region-level CNV track (): Regions affected by CNVs.
- Target-level CNV track (): Targets used for CNV detection.
- Region-level CNV track (
- Additionally, if calculating TMB:
- TMB somatic variants (): Filtered variants that are included in the TMB score calculation.
- TMB somatic variants (
- Additionally, if detecting fusions:
- Unaligned ends (): Unaligned ends mapped to the reference genome.
- Unaligned ends (
- Amino acid changes (