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pure-faf method

pure-faf_workflow

Workflow overview

This workflow is a best-practice workflow for variant filtering of formalin fixed tumour samples. The workflow is built using snakemake and consists of the following steps:

  1. Annotating rhe VCF with a custom panel of normals (PON) This PON has been created from RepSeq samples. Beta distribution testing is performed to identify variants that likely to come from PON.
  2. Applying a general quality filter with creteria including PON, AD and ROQ
  3. Splitting variants into confidence tiers using an AD threshold
  4. Intersecting low-confidence indels with a second tool's indel calls. Intersection is indel type-specific (insertion or deletion), and only position-based (alt allele doesn't matter).
  5. Running microsec twice with different parameters for low-confidence and high-confidence tiers
  6. Merging the results back annotating VCF with microsec results
  7. Applyying different filtering methods on the annotated VCF
  8. Applying a post-filter VAF filter
  9. Quality control using FFPEsig repaired and unrepaired signatures