<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>

CC BY-SA 4.0
2022-04-27T15:48:40.967Z
Thanks, that's clear enough. I'm just looking for a tool to make that easy for me ;-)
Dan Bolser
CC BY-SA 4.0
2022-04-27T15:52:08.983Z
@dan see edit, shapeit4 can impute just a particular region
user438383
CC BY-SA 4.0
2022-04-27T09:59:19.607Z
2022-04-27T16:09:31.337Z
2022-04-27T16:09:31.337Z
user438383
<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>

<snp><imputation><haplotypes><tools>
Imputing small region of the genome
# 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

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## 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.
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

> **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  

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