I wanted to know what you would recommend in two situations:
1)I am running Battenberg for copy number calling however some (~5%) of my SNVs fall in segments that were not given copy numbers by Battenberg. I assume the Tracerx team also ran into the issue that some of their SNVs fell in regions that did not have confident copy number calls by their copy number callers. In this situation, is it fine to assume Copy number A = 1 and Copy number B = 1?
2)I also have some deep targeted sequencing data that doesn't have copy number calls. Due to the limited size of the panel it is difficult to get copy number calls for this data, although I think it still has interesting phylogenetic information due the included SNVs. Can I likewise input Copy number A = 1 and copy number B =1, assuming that Pyclone and conipher tree building can deal with instances where there (sub)clonal deletion as it is built to do?
Or do you think in both cases I should not run CONIPHER on variants that don't have confident copy number calls as this interfere with Pyclone and the tree-building?
Hi,
I wanted to know what you would recommend in two situations:
1)I am running Battenberg for copy number calling however some (~5%) of my SNVs fall in segments that were not given copy numbers by Battenberg. I assume the Tracerx team also ran into the issue that some of their SNVs fell in regions that did not have confident copy number calls by their copy number callers. In this situation, is it fine to assume Copy number A = 1 and Copy number B = 1?
2)I also have some deep targeted sequencing data that doesn't have copy number calls. Due to the limited size of the panel it is difficult to get copy number calls for this data, although I think it still has interesting phylogenetic information due the included SNVs. Can I likewise input Copy number A = 1 and copy number B =1, assuming that Pyclone and conipher tree building can deal with instances where there (sub)clonal deletion as it is built to do?
Or do you think in both cases I should not run CONIPHER on variants that don't have confident copy number calls as this interfere with Pyclone and the tree-building?
Thanks