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Old 03-25-2015, 11:43 AM   #9
Location: Milan

Join Date: May 2013
Posts: 40

Originally Posted by lethalfang View Post
This is an example of an output in my somatic calling pipeline:

Variant Annotation	Gene	Exon	Codon	Chr	Position	Variant	N(A)	N(C)	N(G)	N(T)	T(A)	T(C)	T(G)	T(T)	QSS	Frequency
nonsynonymous SNV	KRAS	exon2	G12A	chr12	25398284	G35C	0	83	0	0	1	37	12	0	57	0.24

N(A), N(C), N(G), and N(T) stand for the number of calls for A, C, G, and T in the normal sample. T(A), T(C), T(G), and T(T) stand for the number of calls for A, C, G, and T in the tumor sample.

So for the normal sample, there are 83 sequences where the base is called C, and 0 for everything else. So it's pretty clear that in the reference and the normal sample, the base is C.
However, in the tumor sample, there are 37 calls for C (reference) and 12 calls for G (variant), so the variant frequency is 12/(12+37) = 0.245.
Notice the variant is labeled G35C. That's because the coding strand is the minus strand, where the DNA reads use the plus strand.
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?
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