Max Somatic VAF

MaxSomaticVaf is a surrogate variant for tumor fraction in ctDNA. The TMB step flags the variants by potential somatic status using database, VAF and clonal hematopoiesis information. The remaining variants are ranked by variant allele frequency in descending order. The variant allele frequency of first COSMIC hotspot (count >50) or confident somatic variant (having significantly shorter fragment size) is reported as the MaxSomaticVaf for each sample. If no such variant exists, the 4th variant is reported.