VanLoo-lab/ascat

ASCAT run without matched normal data

fuzhiliang opened this issue · 1 comments

fuzhiliang commented

Hi,
1、How to calculate logR and BAF in a single sample？
2、Whether the consistency of CNVS detected from without matched normal data and matched normal data has been compared？

tlesluyes commented

Hi @fuzhiliang,

  1. BAF is alt/tot but ASCAT does require tumour/normal pairs to compute logR at SNP positions. If you only have unmatched tumours, you may consider using our (bin-based) ASCAT.sc tool instead (https://github.com/VanLoo-lab/ASCAT.sc).
  2. This hasn't been benchmarked for HTS techniques since ASCAT requires tumour/normal pairs. For SNParrays, I'm not sure I'm fully aware of all of the benchmarking analyses that have been done in the past but we have recently shown a good correlation when getting CN signatures (https://doi.org/10.1038/s41586-022-04789-9 sup fig 6).

Cheers,

Tom.