Figure 8.

Probabilistic bioinformatic filters consistently reduce artefacts. This figure shows the number of false-positive variant calls (y-axis) in four untreated FFPE-DNA replicates processed in two different sequencing centres (C1, C2). ‘No filter’ refers to the total number of false-positive variant calls prior to filtering. The number of false positives was reduced using the probabilistic filter FMC (FilterMutectCalls) of GATK Mutect2 variant calling alone, or in combination with VAF-based filtering (VAF threshold 5% or 10%). All variant calls in this figure are false positives resulting from FFPE-DNA damage or other causes (e.g. sequencing error). Over 100 false positives remain even after combined FMC and 10% VAF-filtering.