Output from Analyze QIAseq DNA
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 '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 detecting CNVs:
- Gene-level CNV track (
): Genes affected by CNVs.
- Gene-level CNV track (
- 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.
- Remove and annotate UMI report (): Summarizes the identified UMIs.
- 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 MSI:
- MSI report (): Contains the MSI Status and the stability of the individual loci.
- MSI report (
- Additionally, if detecting CNVs:
- CNV results report (): Summarizes the identified CNVs.
- CNV results report (
- Additionally, if detecting LOH and HRD:
- Regional ploidy report (): Contains a summary and graphical overview of the detected ploidy states and the underlying CNVs and SNP allele frequencies.
- HRD report (): Contains the HRD, LOH, LST and TAI scores, as well as details for identified regions.
- Regional ploidy report (
- Coverage report raw reads (
- Tracks folder:
- Amino acid changes (
): Amino acid changes introduced by the detected variants.
- Indels indirect evidence (): Filtered indels.
- Inversions (): Identified inversions.
- Long indels (): Identified long 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 detecting LOH and HRD:
- Locus-level ploidy track (): Loci annotated with estimated ploidy states.
- Region-level ploidy track (): Contiguous regions formed of neighboring loci sharing the ploidy state.
- Variants in 15 HRR genes (): Detected variants in the 15 HRR genes:
ATM, BARD1, BRCA1, BRCA2, BRIP1, CDK12, CHEK1, CHEK2, FANCA, FANCL, PALB2, RAD51B, RAD51C, RAD51D, RAD54L.
The variants are also comprised in the full list of filtered variants.
This additional output has been included to facilitate easy inspection of variants in HRR genes.
- Locus-level ploidy track (
- Amino acid changes (