search

Roth-Lab / pyclone

Probabilistic model for inferring clonal population structure from deep NGS sequencing.
https://bitbucket.org/aroth85/pyclone/wiki/Home
Other
98 stars 36 forks source link

ref_count and var_count input for Pyclone #22

Open TnakaNY opened 3 years ago

TnakaNY commented 3 years ago

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 commented 2 years ago

I have the same question.

biginfor commented 2 years ago

But I think it should be t_ref_count and t_alt_count

aroth85 commented 2 years ago

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.