The plot generated by sciClone
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.
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HY
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Chris Miller
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lhaiyan3
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written
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lhaiyan3
1 answer
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.
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