DP meaning in VCF files

Question

[Maryam]

Hello all,

First of all thank you very much for your support because this platform is very useful to get your answers.

I have another question and I really want an answer.

In VCF file 'DP' means Depth and in the VCF file you will see two DPs with different values e.g. one DP is next to 'Qual' and second DP is next to 'AF'. Can someone help me understand what is the difference between these two DP and which one should I choose to say this is my variation DP (Depth)???

Thank you

[iraun]

You mean the DP in the INFO column and DP in SAMPLE(s) column?

[Pierre Lindenbaum]

look for their definitions in the VCF header.

[cpad0112]

if you are looking at overall read depth (DP) i.e across samples in VCF, look at info column. If you are looking at sample specific read depth (DP), look at the order of DP in format column and corresponding value in sample column / field would be read depth (DP).

Answer 1

[Kevin Blighe]

Hello,

I provide a comprehensive answer, here: DP (read depth) in VCF files?

Mit freundlichen Grüßen,

Kevin

[Maryam]

Thank you!