qindan2008

yes, "normal-tumor germline mode" referred to Strelka2's multi-sample germline calling mode and the first sample is normal. 1. The multi-sample germline calling result was: 1 241680511 . T TA 1361...

OK,Thank you.

I met the same problem, when run RunPrestoAll: Warning message: “No DE genes identified” Warning message: “The following tests were not performed: ” Warning message: “When testing Fibroblast versus all:...

How to solve the problem?

I would also be interested in how to extract cluster specific variants.

We have tried to add --pool-genes or changed the default -b option, but none of them succeed. All output files were still empty. Does Alternative splicing can't be analyzed, when...

I updated SCP to version 0.4.7.9000, and still got the same error

When I add sample.names = samples, where samples=c("M1", "M2", "P"), infer.clonal.models turned to be right, no error occurred. Thank you!

I have the same problem. I get CCF with TitanCNA which output CellularPrevalence but no CellularPrevalence_std. How can I get it? Thank you.

In the #84 [(comment).](https://github.com/mskcc/facets/issues/84) comment, "(cnlr.median - dipLogR) is the log(total copy number) unadjusted for purity which is what you want", "the log tcn values, which corresponds to also adjusting...