Copy Number Alteration and Loss or Heterozygosity

Question

[Bogdan]

Dear all,

I would appreciate having a piece of advice :

Given the output from a copy number caller (FACETS, TitanCNA, Sequenza, Sclust) which criteria shall I apply on LogR and BAF (B allele frequency, minor allele frequency) in order to annotate the CNA/LOH as : homozygous deletion, heterozygous deletion, diploid, copy number gain, copy-number amplification, copy-number LOH ?