ref_count and var_count input for Pyclone

[TnakaNY]

Please let me confirm my understanding.

I have a question about ref_count and var_count input data of Pyclone.

In my .maf file, I have columns named "t_alt_count", "t_ref_count", "n_alt_count", "n_ref_count".

Should I use total value of t_ref_count and n_ref_count for ref_count input of Pyclone?

[biginfor]

I have the same question.

[biginfor]

But I think it should be t_ref_count and t_alt_count

[aroth85]

I am not sure of the tool creating the file, but I suspect it should be t_ref_count and t_alt_count. It should be the counts from the tumour sample not the normal.