I have multiple metastatic samples from the same cancer patient. I have used FACETS to call CNVs for each sample. Now, I would like to merge the individual results in a table where each row is a CNV, and each column is a sample.
Because different samples have different segments, I merge the samples by introducing breaks to the segments for each position where there is a CNV start or end in another sample. Example:
sample 1 start-end : copy number
1-100 : 3
101-200 : 1
sample 2 start-end : copy number
1-50 : 4
51-200 : 0
merged start-end : copy number(S1) : copy number(S2)
1-50 : 3 : 4
51-100 : 3 : 0
101-200 : 1 : 0
My question is: Instead of creating artificial breaks, it would be great to be able to narrow overlapping segments from different samples to common CNVs. Are there any previous examples (or tools) where this is done? Or, are there allele specific copy number tools which work with multiple samples, and do clonal heterogeneity analysis?