Output from the Perform QIAseq Multimodal Analysis (Illumina)

The Perform QIAseq Multimodal Analysis workflow produces a large number of files organized into a number of subfolders as well as single elements.

The root folder contains four subfolders (QC & Reports, Tracks (WT), Tracks (Fusions) and VCF exportable tracks) in addition to the following output elements:

The subfolder QC & Reports contain Reports for both the DNA and RNA part of the workflow. Each report has the prefix DNA or RNA as appropriate. The folder includes, among others, the following report types:

The subfolder called Tracks (WT) includes:

The folder Tracks (fusion) contains data related to the fusion chromosomes

The final folder, VCF Exportable Tracks, contains outputs that can be exported together as a single VCF file using the VCF exporter. This folder contains a variant track of variants passing filters, a track of fusions, and, if CNV detection has been run, a CNV target-level track.

The difference between the Unfiltered variant track in the Tracks (WT) folder and the Variants passing filters track depends on the following options available in the filtering steps:

For quality control of fusion calls, see https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Interpretation_fusion_results.html. We particularly recommend carrying out manual quality control checks on results that include fusions with novel exon boundaries.