This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Interpret the read depth in VCF format

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 alignment next-gen
• 7,889 views • link
updated by Ram Ram • written by stat.1405 • stat.1405

1 answer

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.

• 0 views • link
written by Devon Ryan Devon Ryan

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.

• 0 views • link
written by stat.1405 • stat.1405

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.

• 0 views • link
written by Devon Ryan Devon Ryan

Log in to answer this question.

More posts like this