difference between different field info in vcf file format

Question

[rheab1230]

Hello, Does anyone know what the difference between these two field format in vcf file. GT vs DS. I know GT represent genotype information and DS represent dosage info. Can we use them interchangeably, is there any difference between them. I got the dosage info after putting vcf file in michigan imputation server

Answer 1

[Jeremy Leipzig]

these are really Minimac3 tags - "dosage" is not applicable to a normal VCF full of observations

DS : Estimated alternate allele dosage Calculated as p(heterozygous) + 2*p(homozygous alternate)

GT : Estimated most likely genotype

I don't think these are interchangable (one sounds like a probability and the other sounds like a best guess)

Answer 2

[pabe]

GT and DS are not the same.

I suppose you can think of GT as a "hard call" such as 0/0 or 0/1. In your case, minimac uses a maximum likelihood estimator to generate the hard calls.

DS is the estimated alternate allele dosage where [P(0/1)+2*P(1/1)]. It will always have a value between 0 to 2. The dosage value gives an indication of how well the genotype is supported by imputation.

[rheab1230]

Thank you for the response.