Recommended cval value for whole exome sequencing data

mskcc / facets-suite

Utility functions for FACETS

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Recommended cval value for whole exome sequencing data #48

Open hanyin88 opened 2 years ago

hanyin88 commented 2 years ago

Hello,

I would like to ask what would be the recommended cval number for WES data with 40x coverage when using facets-suite? I come across this post (https://github.com/taylor-lab/facets-suite/wiki/1.-Running-FACETS) and would like to check if purity-cval 1000 and cval 500 is still the recommendation. I am asking as these numbers are different than original FACETS facets default based on exome data which is 150 for procSample step.

Deeply appreciate the kind reply!

zh9118 commented 1 year ago

I am having the same question. Glad to see this issue, but so disappointed to see no replies. @hanyin88 did you find out an answer?