Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. This repository includes the updated algorithm, called THetA2.
Dear maintainers,
I was wondering which sets of potential SNPs could and should be used with THetA2. Of course, one can use the Virtual SNP array from http://compbio-research.cs.brown.edu/projects/theta/data/AffySNP6.0_hg19.txt.formatted. Alternatively, one can call germline SNVs on the normal samples and then use those as the SNP set.
Which one would you recommend? Would you imagine it makes a difference?