Answers.Body: <p>Impute2 is a great, if dated choice. Another great choice is <a href="http://faculty.washington.edu/browning/beagle/beagle.html" rel="nofollow noreferrer">beagle</a>. The advantage of beagle in this case is that it is not as strict about requiring a recombination map. Without a map, results will be poorer, but perhaps good enough.</p>
  <p>Do make sure that your sample size including a reference panel is at least 200 in any case.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-05-09T12:06:19.767Z
Answers.LastActivityDate: 2021-06-09T07:13:54.703Z
Answers.LastEditDate: 2021-06-09T07:13:54.703Z
Answers.UserDisplayName: winni2k
Body: <p>I am an undergrad working on a set of genotype matrix of dogs, it's in csv file format with information on only the each sample as rows, chromosome and its position as columns, and the rest of the matrix is filled with 0,1,2 and missing values.</p>
  <p>So I am wondering what would be the best method to impute the genotype with all the data I get? I looked up Impute2, but it seems to require the reference data(recombination map) which I don't have...</p>
  <p>Really appreciate whoever answers my question!!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-09T10:10:51.353Z
Comments.Text: I have never inputted genotype data, but I am pretty sure a recombination map for dogs exists. Check for example here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5100850/
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2021-05-09T15:52:12.010Z
Comments.Text: I've done imputation on dog data before - so I can hopefully help. However, I think we need some more information from you. How many individuals and SNPs do you have to begin with? Are the dogs the same breed or mixed?
Comments.UserDisplayName: user438383
Tags: <imputation>
Title: Imputation of dog genotype
ThreadText: # Imputation of dog genotype
  
  (Asked by: username_0 on 2021-05-08)
  
  I am an undergrad working on a set of genotype matrix of dogs, it's in csv file format with information on only the each sample as rows, chromosome and its position as columns, and the rest of the matrix is filled with 0,1,2 and missing values.
  
  So I am wondering what would be the best method to impute the genotype with all the data I get? I looked up Impute2, but it seems to require the reference data(recombination map) which I don't have...
  
  Really appreciate whoever answers my question!!
  
  **Tags:** imputation
  
  > **Comments:**
  > **username_1**: I have never inputted genotype data, but I am pretty sure a recombination map for dogs exists. Check for example here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5100850/  
  > **username_2**: I've done imputation on dog data before - so I can hopefully help. However, I think we need some more information from you. How many individuals and SNPs do you have to begin with? Are the dogs the same breed or mixed?  
  
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  ## 1 answers
  
  ### Answer by username_3 on 2021-05-09. Score: 2
  
  Impute2 is a great, if dated choice. Another great choice is [beagle](http://faculty.washington.edu/browning/beagle/beagle.html). The advantage of beagle in this case is that it is not as strict about requiring a recombination map. Without a map, results will be poorer, but perhaps good enough.
  
  Do make sure that your sample size including a reference panel is at least 200 in any case.
  
  
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