text: user8875: If I'm looking for a specific SNP in my SNP-Chip data and it isn't there, are there any tools that let me quickly impute that SNP from surrounding SNPs rather than running a lengthy 'whole chromosome' imputation job?
  If so, roughly how many upstream and downstream SNPs are generally required to predict the haploblock 'accurately'?
  
  user3694: I would take something like 1.5Mb either side of the SNP of interest (so a 3Mb chunk), subset that out from the target and reference panel and then perform imputation on that chunk alone. I think that size will give you more than enough LD, since LD decays by about 500kB in most human populations by then.
  shapeit4 has an option to just impute a single region:
  shapeit4 \
      --input unphased.bcf \
      --map chr20.b37.gmap.gz \
      --region chr21:1231213-1413143 \ ## change this bit
      --reference reference.bcf \
      --output phased.bcf
  
  
original_text: 8875: <p>If I'm looking for a specific SNP in my SNP-Chip data and it isn't there, are there any tools that let me quickly impute that SNP from surrounding SNPs rather than running a lengthy 'whole chromosome' imputation job?</p>
  <p>If so, roughly how many upstream and downstream SNPs are generally required to predict the haploblock 'accurately'?</p>
   3694: <p>I would take something like 1.5Mb either side of the SNP of interest (so a 3Mb chunk), subset that out from the target and reference panel and then perform imputation on that chunk alone. I think that size will give you more than enough LD, <a href="https://www.mdpi.com/2073-4425/8/5/133/htm" rel="nofollow noreferrer">since LD decays by about 500kB in most human populations by then.</a></p>
  <p><a href="https://odelaneau.github.io/shapeit4/#documentation" rel="nofollow noreferrer">shapeit4 has an option to just impute a single region</a>:</p>
  <pre><code>shapeit4 \
      --input unphased.bcf \
      --map chr20.b37.gmap.gz \
      --region chr21:1231213-1413143 \ ## change this bit
      --reference reference.bcf \
      --output phased.bcf
  </code></pre>
  