The plot generated by sciClone

Question

[lhaiyan3]

Hi,

I am using the sciClone for the tumor clonality analysis. I got the plot, but my plot is very clean. It did not show any Variant allele frequecy, tumor coverage. When I use this program, I did not get any wrong message. Can anyone please give me some suggestions? Thanks very much.

best

HY

Answer 1

[Chris Miller]

Some things to check:

• Did you have variants that fell into copy number neutral regions?

• Did your variants all meet the minimum depth threshold that was set in the command?

It would also be useful to post your STDOUT from running the tool, the R code you were using, and the head of your input files.