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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.
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?
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