Question: Dp4 Values In Vcf Format???
2
gravatar for Deniz
8.8 years ago by
Deniz210
Deniz210 wrote:
REF     ALT   DP4 values
C       T     0;0;0;3

what does reference forward for C? what does reference reverse for C? alternate forward for T?? alternate reverse for T???

could you explain it?

Thanks

vcf • 4.3k views
ADD COMMENTlink modified 3.9 years ago by Anop Singh Ranawat0 • written 8.8 years ago by Deniz210
4
gravatar for iansealy
8.8 years ago by
iansealy250
iansealy250 wrote:

http://samtools.sourceforge.net/mpileup.shtml says:

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.

So "forward ref alleles" in your case means the number of 'C's called on forward reads, whereas "reverse ref" would be the number of 'C's called on reverse reads. So you have three 'T's, all from reverse reads.

ADD COMMENTlink written 8.8 years ago by iansealy250
0
gravatar for Anop Singh Ranawat
3.9 years ago by
India
Anop Singh Ranawat0 wrote:

variant allele frequency (VAF), to determine, whether it is heterozygous or homozygous, use DP4 field. DP4 is Number of 1) forward ref alleles; 2) reverse ref; 3) forward non-ref; 4) reverse non-ref alleles, used in variant calling.

VAF = (forward non-ref + reverse non-ref alleles) / (forward ref alleles + reverse ref + forward non-ref + reverse non-ref alleles)

so you can calculate allele frequency .........

ADD COMMENTlink written 3.9 years ago by Anop Singh Ranawat0
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