I have been trying to use PyClone (https://www.nature.com/articles/nmeth.2883#abstract) to do subclonal mutational analysis on whole genome sequencing data of cell lines, but because the coverage is only 25X, am having a hard time using PyClone.
I set some read depth filters to decrease which mutations to analyze using PyClone because the pipeline was taking too long to run on the entire list of mutations called (~4.5 million).
Are there any available pipelines for subclonality analysis on data with low coverage?
I set some read depth filters to decrease which mutations to analyze using PyClone because the pipeline was taking too long to run on the entire list of mutations called (~4.5 million).
Are there any available pipelines for subclonality analysis on data with low coverage?