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!
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