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Old 12-12-2018, 11:22 AM   #1
esh81
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Location: Ohio

Join Date: Dec 2018
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Default Pipelines for identifying subclonal mutational events in WGS with 25X coverage

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?
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