Reduce the impact of deamination in low-quality FFPEs
Samples of low quality that exhibit deamination can be analyzed if you increase the minimum allele frequency in an analysis workflow. For example, a minimum allele frequency of 10% for the tumor mutational burden (TMB) calculation can reduce the impact of deamination on the reported TMB value. It is important to consider the tumor content of a given sample when you increase the minimum allele frequency of the TMB calculation.
Samples with low tumor content can have many true somatic mutations that are excluded from the tumor mutational burden calculation when a higher minimum allele frequency filter is included in the analysis workflow.
The tumor mutational burden values cannot be reliable if you adjust the minimum allele frequency parameters for samples with a high estimated SNP proportion consistent with deamination, (primarily an FFPE number) or a high deamination score, (for example >100).
IMPORTANT! Use the default parameter settings unless you are an advanced user.