KarchinLab/pictograph

How to infer "multiplicity" value

Tato14 opened this issue · 1 comments

Tato14 commented

Thanks for the great tool!

I have multi-sample data from several patients. The data was obtained using a Foundation like NGS panel (not WES or WGS). I can more or less infer the copy number of each mutation but I am unsure how to get the "multiplicity" value. Is there any way to calculate it? Is like a rule of thumb? I see in your example that most of the cases with a multiplicity = 2 are the ones with alt_reads > 0.5*total_reads, but I would like to confirm how you get this info.

Thanks!

jiaying2508 commented

Multiplicity refers to the number of copies carrying the mutation. We have a script written to infer multiplicity. For your input data, if you don't include "multiplicity" column in the heading, then the multiplicity will be computed automatically.

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