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Description of inputs
Start: Genome basepair of start of copy number segment.
End: Genome basepair of end of copy number segment.
Chromosome: Chromosome of copy number segment.
f: Mean allele fraction of minor parental allele at this segment. This corresponds to the allele imbalance observed in inherited (germline) SNPs at this locus. For example a one copy amplification would yield a 2:1 ratio of parental alleles the germline variants within a segment of this locus would be centered around 0.66 and 0.33 allele fractions. As a matter of convention f represents the minor fraction (0.33).
tau: Two centered segment copy ratio data. Copy ratio is the relative amount of DNA in the tumor sample at the segment compared to normal (or a panel of normals). We use this ratio plus 2.
Taylor-Weiner, A. et al. DeTiN: overcoming tumor-in-normal contamination. Nat. Methods 15, 531–534 (2018).