Fig 1.
General workflow of variant interrogation in tumor samples.
Please note that the steps are intended to be taken sequentially, and each should be completed before moving on to the next; however, depending on how data has been processed prior to your work, it may be necessary to start later in the pipeline. Created in BioRender. Arseneau, R. (2026) https://BioRender.com/armq9mn.
Table 1.
Key terms and concepts.
Table 2.
Summary of sequencing approaches for variant detection.
Table 3.
Common sequencing file types and their structure.
Fig 2.
Flowchart of common sequencing file types and analysis stages.
The diagram illustrates the typical file types encountered throughout the sequencing and analysis pipeline, progressing from raw data (left) to results (right). File types are grouped by processing phase: green (Phase 1: Planning and pre-processing), yellow (Phase 2: Variant calling and annotation), and blue (Phase 3: Filtering and validation). Solid arrows indicate the standard forward progression of file generation, while dotted arrows represent steps where data can be reverted to a previous file type. The objective is to complete the pipeline, transforming raw reads into interpretable variants. Created in BioRender. Arseneau, R. (2026) https://BioRender.com/wx6ql68.
Table 4.
Variant Caller information.
Table 5.
Commonly used pathogenicity predictors.
Fig 3.
Example variant prioritization scheme.
The flowchart illustrates a strategy for prioritizing variants into four bins based on predicted pathogenicity. Variants are initially assigned to a bin using criteria including ClinVar annotations, COSMIC frequency, and SpliceAI scores. Variants may then be reclassified to a different bin based on additional pathogenicity criteria, such as Franklin classifications (for promotion from Bin 2 to Bin 1), or other computational predictors including CADD, REVEL, and phastCons conservation scores (for promotion from Bin 4 to Bin 3, or Bin 3 to Bin 2). Bin 1 contains pathogenic variants, Bin 2 contains likely pathogenic variants, Bin 3 contains variants of uncertain significance (VUS), and Bin 4 represents likely benign or benign variants. Created in BioRender. Arseneau, R. (2026) https://BioRender.com/o4pbmzu.
Table 6.
Variant reporting checklist.
Table 7.
Code reproducibility and sharing checklist.