WES and average depth ~100

[henan zhu]

Hello,

I am would like to feed Pyclone with whole-exome sequencing data (~100x). I noticed that PyClone usually uses deep sequencing data, so I am wondering if it is possible to run Pyclone on 100x WES data. If possible, do I need to set a cutoff like VAF > 0.05, depth > 30?

Thanks,

Henan

[Andrew]

Hi Henan,

There is no real depth restriction. However, your ability to resolve clones will be limited. This is especially true if you only have single sample data. This isn't really a limitation of PyClone per se, and affects most methods for clonal deconvolution.

No special thresholds are needed. 

Best wishes,

Andy