Output from the Perform TSO500 DNA Analysis

The Perform TSO500 DNA Analysis (Illumina) workflow output has been ordered into a number of single key elements and folders with different purpose.

  1. QC & Reports: A folder that contains the following reports.
    • DNA_remove_and_annotate_with_UMI_report: Contains information about the number of reads being processed and the number and fraction of reads with UMIs.
    • DNA_trim_reads_report: Contains detailed trimming results and information about automatic adapter read-through trimming.
    • DNA_UMI_read_report: A comprehensive report containing statistical metrics and graphical representations on UMI reads. Focus is on duplex, read grouping, read quality and read length distribution.
    • DNA_mapping_report: Contains information on mapping statistics.
    • DNA_remove_ligation_artifacts_report: Summarizes any ligation and common sequence artifacts found in and removed from the read mapping.
    • DNA_structural_variant_caller_report: Gives an overview of the numbers and types of structural variants found in the sample.
    • DNA_variant_report: Summarizes variants detected in the read mapping.
    • Coverage_report: Contains statistical metrics of the covered targets.
    • TMB_report: Contains information on variant distribution and coverage for detecting the TMB score as well as the score itself.
    • CNV_results_report: Contains statistical metric on the CNV analysis. This output only exists when control sample(s) are provided.
    These reports are summarized in the output called DNA_combined_report, which is useful for quick QC assessment.

  2. Tracks: A folder that contains the following tracks.
    • Mapped_UMI_reads: The read mapping produced by mapping the UMI reads.
    • Unfiltered_variants: All variants called by the Low Frequency Variant Detection tool.
    • Indels-Indirect_evidance: Indels inferred from indirect evidence by the Structural Variant Caller and not detected by the Low Frequency Variant Detection tool.
    • Amino acid track: Track of amino acids sequences and changes introduced by the detected variants.
    • TMB_somatic_variants: Variants included in the TMB score estimation.
    • Per-region_statistics_track: Coverage report of the covered target region.
    • Gene_level_CNV_track: Contains CNV evidence per gene. This output only exists when control sample(s) are provided.
    These elements are compatible with the Track List that in addition contains VCF Exportable Tracks element described in item 3 and reference elements from the CLC_References location (Reference sequence, Genes, CDS and mRNA). The Track List is helpful for visual inspection of variants and CNV regions.

  3. VCF Exportable Tracks: The VCF Exportable Tracks folder contains outputs that can be exported together as a single VCF file using the VCF exporter. The tracks found in the VCF Exportable Tracks folder can also be exported as a single VCF together with the Final_fusion_genes (WT) from the RNA part of the pipeline.
    • Variants_passing_filters: All variants of high enough quality to be kept. As this track contains the possible driver mutations, it is the track selected for VCF export rather than the TMB somatic variant track.
    • Region-level_CNV_track: CNV track with information on regions rather then genes. The region-level annotation track provides CNV breakpoints that are useful for export. This output only exists when control sample(s) are provided.