I ran phylogicNDT through Terra a few days ago and when reviewing output noticed that indels with high ccf (for example ccf_hat of > 0.9 across multiple samples per participant) are not assigned back in for output after they are initially removed for clustering. I would be grateful for your input as to whether this was done intentionally (i have previously run the same samples a few months ago and the indels were included in the output at that time) and also for more education on why indels are specifically removed prior to clustering. Thanks!
Hi,
I ran phylogicNDT through Terra a few days ago and when reviewing output noticed that indels with high ccf (for example ccf_hat of > 0.9 across multiple samples per participant) are not assigned back in for output after they are initially removed for clustering. I would be grateful for your input as to whether this was done intentionally (i have previously run the same samples a few months ago and the indels were included in the output at that time) and also for more education on why indels are specifically removed prior to clustering. Thanks!
Alok