Dp4 Values In Vcf Format???

Question

[Deniz]

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

Answer 1

[iansealy]

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.

Answer 2

[Anop Singh Ranawat]

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 .........