Question: Interpret the read depth in VCF format
0
gravatar for stat.1405
5.2 years ago by
stat.140520
uk
stat.140520 wrote:

what is the different beween 

  • DP combined depth across samples, e.g. DP=154  - In INFO field.
  • DP read depth at this position for this sample (Integer) - In Genotype field.

It is VCF format..

 

snp next-gen alignment • 3.4k views
ADD COMMENTlink modified 2.5 years ago by Biostar ♦♦ 20 • written 5.2 years ago by stat.140520
2
gravatar for Devon Ryan
5.2 years ago by
Devon Ryan91k
Freiburg, Germany
Devon Ryan91k wrote:

The explanation is contained within the descriptions you posted. One is the within sample depth, the other the depth across samples. If your VCF file only contains a single sample, then these values will be the same. If not, then they'll obviously differ.

ADD COMMENTlink written 5.2 years ago by Devon Ryan91k

what I understand from your answer the first DP is for all of the sample at a position.

and the DP in genotype field is the read depth for a sample. If so, the INFO DP should be equal to the sum of DP at the same position.

in my data I have 20 sample. but the sum of their dp not equal to the dp in info field.

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by stat.140520
1

How depth, both per-sample and in toto, is calculated can vary by algorithm. Check the details (likely the source code, since it wouldn't surprise me if this isn't documented) of whatever program you used to call the variants.

ADD REPLYlink written 5.2 years ago by Devon Ryan91k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 772 users visited in the last hour