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.

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.

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