I would like to analyze my RNA seq profiles from bulk tissue samples (Paired-End, 50M reads/sample, tumour-normal pairs) with varscan2 to detect mutations. Then I would like to use those detected mutations to estimate presence of different tumour clones (likewise pyclone on WGS data). Therefore my questions:
1.Is it possible to estimate number of clones and clonal abundancy from RNA seq profiles from bulk tissue? and if yes: are 50M reads/sample enough coverage.
2.Could you recommend which package to use for this, for example is pyclone suitable for this? Thank you in advance for the advice!