count number of A,C,G,T using DP4 in VCF

[jomaco]

Did anyone have any luck finding an answer to this?

Thanks

[jomaco]

Did anyone have any luck finding an answer to this?

Thanks

[Tally]

T is 7, forward A/G is 33, reverse A/G is 81, C is 0

I don't think there is any way of knowing how many G's and A's from DP4, because these are both lumped under 'non-reference'. Have a look at that position in the alignment using tview to confirm this.

If someone knows of a way to obtain this information from mpileup I would also be very interested to know, as it would be hard to call the right SNP at this location without it.

[aslihan]

Could you answer this question? I have also similar question?

[gcrdb]

Hi,
Not sure about DP4 format in VCF of A,C,G,T count
chr1 90119 . T G,A,X 99 . DP=121;AF1=1;CI95=1,1;DP4=0,7,33,81;MQ=51;PV4=0.19,1,1,0.064 PL 255,208,255,255,0,255,255,255,255,255


Which one is correct? (Total DP=121= 7+33+81 seems okay.)
T is 7, G is 33 , A is 81 , C is 0
T is 7, A is 33 , G is 81, C is 0
T is 77, forward A/G is 33, reverse A/G is 81, C is 0


How about this one?
chr4 1808445 . C T,G,A 99 . DP=459;AF1=1;CI95=1,1;DP4=33,55,260,108;MQ=31;PV4=1.3e-08,3.1e-44,1,4.3e
-05 PL 186,164,255,255,0,255,255,255,255,255
I guess: C=33+55, but how many T,G,A ?? Help please.

thanks,


According to http://samtools.sourceforge.net/mpileup.shtml

DP4 is:
Number of 1) forward ref alleles; 2) reverse ref; 3) forward non-ref; 4) reverse non-ref alleles, used in variant calling. Sum can be smaller than DP because low-quality bases are not counted.