I want to use PyClone using Single Nucleotide Variants called from Whole-exome sequencing of matched primary and metastatic tissue samples.
I do not have copy number data, and the PyClone usage page says:
If you do not major and minor copy number information you should set the minor copy number to 0, and the major copy number to the predicted total copy number. If you do this make sure to use the total_copy_number for the --var_prior flag of the build_mutations_file command. DO NOT use the parental copy number information method as it assumes you have knowledge of the minor and major copy number.
I have two questions:
1) Can I predict total copy number with Whole-exome sequencing data?
2) If not, is it sensible to set the major copy number to 2?