Hi All,
could there be any reasonably reliable SNV calling approach in the following scenario: I have shallow (1-3x) WGS sequencing data from liquid biopsy samples from cancer patients, where the ctDNA fraction is very low (1% AF) and that contains the SNVs that I would be interested in. I don't have the white blood cell (aka normal sample) data for the patients, just the pure, sequenced blood plasma (mix of cfDNA + ctDNA).
I know, it's not a great setup, but this is what I've got to work with for a project.
Any suggestion (even if it's just talking me out of doing something crazy like this) is appreciated!
Thanks!
could there be any reasonably reliable SNV calling approach in the following scenario: I have shallow (1-3x) WGS sequencing data from liquid biopsy samples from cancer patients, where the ctDNA fraction is very low (1% AF) and that contains the SNVs that I would be interested in. I don't have the white blood cell (aka normal sample) data for the patients, just the pure, sequenced blood plasma (mix of cfDNA + ctDNA).
I know, it's not a great setup, but this is what I've got to work with for a project.
Any suggestion (even if it's just talking me out of doing something crazy like this) is appreciated!
Thanks!