text: user10296: I'm following this 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. I'm including the vcf files 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.
  
  user3694: 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.
  
original_text: 10296: <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>
   3694: <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>
  