Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-04-27T15:48:40.967Z
Answers.Text: Thanks, that's clear enough. I'm just looking for a tool to make that easy for me ;-)
Answers.UserDisplayName: Dan Bolser
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-04-27T15:52:08.983Z
Answers.Text: @dan see edit, shapeit4 can impute just a particular region
Answers.UserDisplayName: user438383
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-04-27T09:59:19.607Z
Answers.LastActivityDate: 2022-04-27T16:09:31.337Z
Answers.LastEditDate: 2022-04-27T16:09:31.337Z
Answers.UserDisplayName: user438383
Body: <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>
  
Tags: <snp><imputation><haplotypes><tools>
Title: Imputing small region of the genome
ThreadText: # Imputing small region of the genome
  
  (Asked by: username_0 on 2022-04-27)
  
  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'?
  
  **Tags:** snp, imputation, haplotypes, tools
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2022-04-27. Score: 3
  
  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.](https://www.mdpi.com/2073-4425/8/5/133/htm)
  
  [shapeit4 has an option to just impute a single region](https://odelaneau.github.io/shapeit4/#documentation):
  
  ```
  shapeit4 \
      --input unphased.bcf \
      --map chr20.b37.gmap.gz \
      --region chr21:1231213-1413143 \ ## change this bit
      --reference reference.bcf \
      --output phased.bcf
  
  ```
  
  > **Comments:**
  > **username_0**: Thanks, that's clear enough. I'm just looking for a tool to make that easy for me ;-)  
  > **username_1**: @dan see edit, shapeit4 can impute just a particular region  
  
  ---
  
  