Question About DP4

Question

[mdr45]

Hello,

I have a pretty simple question that I wasn't able to find an answer to looking through the existing questions:

For the DP4 values in the INFO field of a vcf file, I understand that the first two values are forward and reverse counts corresponding to the reference variant, and the next two are forward and reverse counts corresponding to alternate alleles. My question is: if there is more than one alternate allele, do the last two numbers represent the sum of counts from all alternate alleles of sufficient quality (which was my initial assumption) or do they represent only counts for the alt allele that was most common in the samples? I tried reading the documentation but was unable to find anything addressing this specific point.

Regards,

~Mertain

Answer 1

[Kevin Blighe]

I think that the best thing to do is to load your BAM into IGV, ensure that all mapped reads are displayed, and then literally count the number of variant and ref alleles over the position of interest, and then corroborate with the values in DP4 in your VCF.

I would imagine that the final 2 numbers in DP4 relate to counts of all possible alternate alleles - that is just my natural assumption. It would not make sense to only tally read-depth over 1 or another of the alternate alleles.