Question

difference between different field info in vcf file format

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Entering edit mode

2.3 years ago

rheab1230 ▴ 140

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

format GT vcf filr DS • 1.6k views

ADD COMMENT • link 2.3 years ago by rheab1230 ▴ 140

score 2 · Accepted Answer · 2022-08-29

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)

score 2 · Accepted Answer · 2022-08-29

2

Entering edit mode

2.3 years ago

pabe ▴ 30

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.