<p>It seems that you didn't use the following flag:</p>
<pre><code> --impute-reference-only-variants   Allows imputation at variants only present
                                     in the reference panel. The use of this 
                                     option is intended only to allow 
                                     imputation at sporadic missing variants. 
                                     If the number of missing variants is 
                                     non-sporadic, please re-run the genotype 
                                     likelihood computation at all reference 
                                     variants and avoid using this option, 
                                     since data from the reads should be used. 
                                     A warning is thrown if reference-only 
                                     variants are found.
</code></pre>
<p>You were expecting additional SNPs which were present in the reference panel to be imputed into your targets, but you didn't include the flag <code>--impute-reference-only-variants</code>, so only individual missing genotypes were imputed. Individual missing genotypes <code>./.</code> are always imputed if they are present in both the target and reference, but if the SNP is present in the reference and not the target, it won't be unless you use that flag.</p>

CC BY-SA 4.0
2022-01-01T11:42:23.443Z
Doesn't answer my question. Can u explain it clearly?
Shafayet Rahat
CC BY-SA 4.0
2022-01-01T11:57:54.240Z
You mean without --impute-reference-only-variants  it will give me only phased data of the sample? Not the imputed snps from reference?
Shafayet Rahat
CC BY-SA 4.0
2022-01-01T13:03:02.177Z
Can you explain your answer more elaborately? I didn't fully understand the answer .
Shafayet Rahat
CC BY-SA 4.0
2022-01-01T13:05:48.443Z
@ShafayetRahat With all due respect, the function of SE isn't to provide a tutorial service for everything you might not totally understand, especially when you say 'I don't understand' rather than being specific about *what* you don't understand. I feel like my answer provides a clear answer to the question you gave. Having to respond to multiple additional questions in the comments gets a bit tiresome after a while and doesn't;t motivate me to answer other questions you might ask.
user438383
CC BY-SA 4.0
2022-01-01T13:16:23.463Z
sorry about that. Actually, I'm at learning period. So, it may seem that I was asking for a tutorial service. But, in reality, I'm just stuck in the process. I guess the purpose of the whole stack exchange community is for helping with a problem to solve it. It's not like you are bound to answer the question or something like that. You can choose not to answer the question. Anyway, my point is I'm not treating anyone as my personal instructor. I'm very sorry if any of my conversations hurt anyone. And once again sorry for your inconvenience.
Shafayet Rahat
CC BY-SA 4.0
2022-01-01T11:33:21.030Z
2022-01-01T13:02:42.970Z
2022-01-01T13:02:42.970Z
user438383
<p>I'm following <a href="https://odelaneau.github.io/GLIMPSE/tutorial_b38.html" rel="nofollow noreferrer">this</a> tutorial of GLIMPSE for learning. I was expecting some extra SNPS coming from the 1000 genome reference in the resulting .vcf file. Though I understand the phasing in the output resulting .vcf, what I don't understand is the imputed result. Apparently the .vcf before and after has the same number of SNPs. I ran the scripts from <a href="http://github.com/odelaneau/GLIMPSE/tree/master/tutorial" rel="nofollow noreferrer">here</a>. I'm including the <a href="https://drive.google.com/drive/folders/1-Jc6b6wMK1RJVtgnLNam-QCJoTjWrTcL?usp=sharing" rel="nofollow noreferrer">vcf files</a> before and after imputation.</p>
<p>Can anyone explain me where the imputed SNPs are in the output v.cf file. If my concept is wrong can anyone tell me what should we expect in result.</p>

CC BY-SA 4.0
2022-01-01T11:32:35.477Z
Please share the exact command you used.
user438383
CC BY-SA 4.0
2022-01-01T11:40:46.367Z
Just run the scripts from https://github.com/odelaneau/GLIMPSE/tree/master/tutorial
Shafayet Rahat
CC BY-SA 4.0
2022-01-01T11:49:54.210Z
Please paste them into the question to make it easier for myself and others to know exactly what you did. Questions should be as self-contained as possible, a external links break.Thank you.
user438383
<vcf><imputation><phasing><1000genomes>
Interpreting imputation result from GLIMPSE
# Interpreting imputation result from GLIMPSE

(Asked by: username_0 on 2022-01-01)

I'm following [this](https://odelaneau.github.io/GLIMPSE/tutorial_b38.html) tutorial of GLIMPSE for learning. I was expecting some extra SNPS coming from the 1000 genome reference in the resulting .vcf file. Though I understand the phasing in the output resulting .vcf, what I don't understand is the imputed result. Apparently the .vcf before and after has the same number of SNPs. I ran the scripts from [here](http://github.com/odelaneau/GLIMPSE/tree/master/tutorial). I'm including the [vcf files](https://drive.google.com/drive/folders/1-Jc6b6wMK1RJVtgnLNam-QCJoTjWrTcL?usp=sharing) before and after imputation.

Can anyone explain me where the imputed SNPs are in the output v.cf file. If my concept is wrong can anyone tell me what should we expect in result.

**Tags:** vcf, imputation, phasing, 1000genomes
> **Comments:**
> **username_1**: Please share the exact command you used.  
> **username_0**: Just run the scripts from https://github.com/odelaneau/GLIMPSE/tree/master/tutorial  
> **username_1**: Please paste them into the question to make it easier for myself and others to know exactly what you did. Questions should be as self-contained as possible, a external links break.Thank you.  

---

## 1 answers

### Answer by username_1 on 2022-01-01. Score: 2 | Accepted answer

It seems that you didn't use the following flag:
 --impute-reference-only-variants   Allows imputation at variants only present
                                     in the reference panel. The use of this 
                                     option is intended only to allow 
                                     imputation at sporadic missing variants. 
                                     If the number of missing variants is 
                                     non-sporadic, please re-run the genotype 
                                     likelihood computation at all reference 
                                     variants and avoid using this option, 
                                     since data from the reads should be used. 
                                     A warning is thrown if reference-only 
                                     variants are found.

You were expecting additional SNPs which were present in the reference panel to be imputed into your targets, but you didn't include the flag --impute-reference-only-variants, so only individual missing genotypes were imputed. Individual missing genotypes ./. are always imputed if they are present in both the target and reference, but if the SNP is present in the reference and not the target, it won't be unless you use that flag.

> **Comments:**
> **username_0**: Doesn't answer my question. Can u explain it clearly?  
> **username_0**: You mean without --impute-reference-only-variants  it will give me only phased data of the sample? Not the imputed snps from reference?  
> **username_0**: Can you explain your answer more elaborately? I didn't fully understand the answer .  
> **username_1**: @ShafayetRahat With all due respect, the function of SE isn't to provide a tutorial service for everything you might not totally understand, especially when you say 'I don't understand' rather than being specific about *what* you don't understand. I feel like my answer provides a clear answer to the question you gave. Having to respond to multiple additional questions in the comments gets a bit tiresome after a while and doesn't;t motivate me to answer other questions you might ask.  
> **username_0**: sorry about that. Actually, I'm at learning period. So, it may seem that I was asking for a tutorial service. But, in reality, I'm just stuck in the process. I guess the purpose of the whole stack exchange community is for helping with a problem to solve it. It's not like you are bound to answer the question or something like that. You can choose not to answer the question. Anyway, my point is I'm not treating anyone as my personal instructor. I'm very sorry if any of my conversations hurt anyone. And once again sorry for your inconvenience.  

---

