T-cell lymphoma call stats - two sequencing runs

Run 1 (with control, but with oxidation/contamination issues) vs. run 2 (tumor-only, improved pipeline)

Objective

• Compare number of coding calls found in run 1 of T-cell lymphoma sequencing (2016) with those found in run 2 (run with the tumor-only pipeline, ultimo 2018), i.e. how many of the coding calls found using matched control do we still find with the new tumor-only pipeline?
• Both runs were performed using Agilent Exome Capture kit v5 (needs confirmation)
• Important notes regarding run 1:
  • It was associated with oxidation artefacts and contamination problems among the control samples
  • Calls considered in this report satisfy three conditions:
    1. They are associated with strong call confidence (called by both MuTect and Strelka),
    2. They are annotated as unlikely caused by an oxidation artefact (or none at all) - results from ad-hoc filtering by DV
    3. They are found in exonic regions (i.e. coding variants)

Results