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smalikic / B-SCITE

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VAF calculation #2

Closed byoo closed 6 years ago

byoo commented 6 years ago

https://github.com/smalikic/B-SCITE/blob/d62f451e0210b6117a27a0d8aa56cf84361ec508/src/Mutation.h#L20

Thank you for sharing B-SCITE. I have a questions about VAF calculation. I wonder why 2 is multiplied to numerator. Would you help me understand the VAF calculation? Thank you.

smalikic commented 6 years ago

Wherever VAF is mentioned in the current version of the code, it refers to 2*var_reads/(var_reads + ref_reads) and should not be mistaken for variant allele frequency used in the literature and defined as var_reads/(var_reads + ref_reads).

byoo commented 6 years ago

Thanks a lot for your prompt advice! What does VAF stand for in this context?

smalikic commented 6 years ago

The meaning of the formula is: expected fraction of cells harbouring mutation. The term VAF does indeed originate from "variant allele frequency" - we should consider doubleVAF or ECF in the future as alternatives to the currently used VAF. Thanks for pointing to this. Hope that these answer your question.

byoo commented 6 years ago

I see. It's like tumor purity. Thanks again for your kind explanation!