GT 2/3, or 3/3 or 2/2 in vcf
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4.2 years ago
Tania ▴ 180

Hi everyone

In human data, what does GT 2/3, or 3/3 mean? Does it mean 3 alt alleles maybe and also 2 ,3 for the reference? I used hg38?

Thanks

vcf • 3.8k views
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Hello Tania!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

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None of the above is answering me. Why rush to close it? !!! Not asking about 0/0 0/1 etc. In your second link Devon is questioning So 2/0 is ACAC/A and 2/1 is ACAC/ACACAC. You only have two alternate alleles shown, so there should be no 3/? in there. This is basically a modified VCF format.

which is my question, I have 3?

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Devon got the answer. A: Meaning Of Genotype 2/0 And 2/1

3: Third alternate allele

Please read the VCF spec.

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In the ref? Not the alt? I am missing something I understand 1/3 but not 2/3 or 3/3 not the first time to read the spec.

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so you have 4 alleles. REF is 0 and your column ALT should contain 3 alleles (1,2 and 3). So a genotype '1/3' is heterozygous diallelic with allele index 1 and allele index 3.

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I am not asking about 1/3 i swear :) You answer what I am not asking about and rush to close the thread !!!

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Hi Tania I think I understand your question. I think you assume that the reference is the first entry and this confuses you that you assume GT should be 0/1 or 1/1 or 1/2 or 1/3 etc like the first one is usually 0 or 1? Right? Because I was there too :) These are indeces so in Devon answer 0 is ref, 1 is first alt and 2 is second alt so on. So when you see 2/3 it means the second alt and the third alt. it doesn't mean its second ref and the third alt. Does this match your thoughts?

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Thanks so much Sharon !

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ok, I reopened the question (please do not delete it)

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Tania : Please do not delete threads once they have received comments/answers.

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Please don't close thread before understanding the question ! You are free to close and I am not free to delete !

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You complained about the fact is was closed. I acknowledged you request and reopened the question.

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Thanks Pierre Lindenbaum !

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This thread was not closed. You were being asked not to delete it since at least three people have offered comments/answers. Deleting a thread is ok if you made a mistake in the original question (and there were no comments/answers offered) but otherwise it is disrespectful to people who are trying to help you.

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@genomax. I closed it at the beginning (as a 'duplicate')

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4.2 years ago

a region of DNA may have several alleles across different individuals, for example you could have any of the bases changed ( three options) but also insertions, deletions all happening at that location.

The possible observed alleles are in the ALT column. The GT columns show which one of those is present in the sample.

for a file that has 2/3 listed it means the sample has the second and third alleles.

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To give you an example if the row that you have has

20     1110696     rs6040355      A      G,T,C

listed then GT=2/3 means that in your sample you have a heterozygous mutation where the A is substituted by T in some DNA reads and by C in others.

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Thats very clear now. Thanks so much Istvan.

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4.2 years ago
Lemire ▴ 940

From the vcf specification:

"GT genotype, encoded as alleles values separated by either of ”/” or “|”, e.g. The allele values are 0 for the reference allele (what is in the reference sequence), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on."

The ALT alleles are in this case separated by commas, such as in

20     1110696 rs6040355 A      G,T     67   PASS   NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2   2/2:35:4

In your case, you must have had a variant with 3 alleles listed in ALT.

source: https://www.internationalgenome.org/wiki/Analysis/vcf4.0/

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yes, i understand, what you mentioned would be 1/2 or 1/3 but what does 2/2 or 2/3 mean? I mean when we have GT is 2/2 in one row and in another case we have GT is 2/3

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To understand the context, could you please post the two lines ? In the mean time, refer to Devon's answer and subsequent discussion on this post: Meaning Of Genotype 2/0 And 2/1 @ Tania

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