How to get per sample read depth from VCF with no DP field

Question

[Rubal]

Hello Everyone,

I have a VCF file that has no DP info only AD (allelic depth). Does anyone know of a way that I can get per sample mean read depth using only the AD filter?

I could write a custom script that sums the two AD values for each site, but I'd be more comfortable if there was a standard tool available (and it would save a lot of time).

example for two individuals:

GT:AD   0|1:6,5 0|0:12,0

Thank in advance!

Answer 1

[chen]

AD = Allele Depth, is not enough to calculate depth

If you don't have DP, you need RD = Reference Depth

[Rubal]

Thanks for the reply that's good to know. Why isn't Allele Depth sufficient, I assumed if you add the counts from both alleles you would get the read depth.

Answer 2

[chen]

Allele Depth is the depth for ALT, and REF is not included

[GenoMax]

This belongs under the comment from @Rubal above.

[hellbio]

I would like to discuss more about the allele frequency spectrum thread at (https://www.biostars.org/p/101218/). Could you share your email address. It would help a lot. Thanks