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Old 03-25-2015, 11:46 AM   #10
lethalfang
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Location: San Francisco, CA

Join Date: Aug 2011
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Quote:
Originally Posted by vd4mindia View Post
I would just want to ask you in case you have have not other bases as 0 in normal in that case do you still calculate the variant allele frequency as the above? Variant allele frequency should be always considered for the reads having variant allele for the tumor sample divided by the total reads at that variant site? Right? Irrespective of the reads falling for other bases in normal samples as well right?
I considered "variant allele frequency" as the frequency of variant alleles in a given sample.
So the tumor's variant allele frequency does not care what's in the normal tissue, and vice versa.
That way, you can monitor the change in variant allele frequency between the tumor and the normal.
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