Body: <p>everyone!</p>
  <p>I'm working with haplotype inference algorithms in pedigree genotype data, and I would like to know if there is a tool or script to calculate switch errors on phased pedigree data (Plink formatted)?</p>
  <p>I already know that VCFtools and other scripts do exist, but they only work with VCF format.</p>
  <p>Note: I tried to convert my phased pedigree data to VCF but I lost phase, so, this approach does not seem to be helpful, that's why I'm looking for a specific tool to detect switches on phased pedigree data.</p>
  <p>A switch errors ocurr when heterozygous positions are misassigned relative to the previous heterozygous position.</p>
  <p>See visual example (block 2), True haplotypes up, inferred haplotypes bottom:
  <a href="https://www.researchgate.net/publication/310766263/figure/fig13/AS:431688409980932@1479933945501/Illustration-of-switch-errors-and-block-breakpoints-In-haplotype-block-2-there-are-two.png" rel="nofollow noreferrer">https://www.researchgate.net/publication/310766263/figure/fig13/AS:431688409980932@1479933945501/Illustration-of-switch-errors-and-block-breakpoints-In-haplotype-block-2-there-are-two.png</a></p>
  <p>In my case, I got the phased pedigree plink file as follows:</p>
  <p>Infered Haplotype, individual 1:
  1|2 2|1 1|2 1|2 1|2</p>
  <p>Real Haplotype, individual 1:
  1|2 1|2 2|1 1|2 1|2</p>
  <p>We can see 2 switches, between position 1-2 and 3-4.</p>
  <p>Thank you very much in advance!
  Regards!</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-03-07T14:43:29.120Z
Comments.Text: Can you explain what switch errors are?
Comments.UserDisplayName: Dan Bolser
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-03-08T18:13:12.080Z
Comments.Text: A switch errors occur when heterozygous positions are misassigned relative to the previous heterozygous position. 
  
  See visual example (block 2), True haplotypes up, inferred haplotypes bottom:
  https://www.researchgate.net/publication/310766263/figure/fig13/AS:431688409980932@1479933945501/Illustration-of-switch-errors-and-block-breakpoints-In-haplotype-block-2-there-are-two.png
  
  I got the phased pedigree plink file as follows:
  
  Inferred Haplotype, individual 1:
  1 1|2 2|1 1|2 1|2 1|2
  
  Real Haplotype, individual 1:
  1 1|2 1|2 2|1 1|2 1|2
  
  See 2 switches, between pos. 1-2 and 3-4.
Comments.UserDisplayName: Roa.tar
Tags: <errors><haplotypes><phasing><pedigree>
Title: How to calculate switch errors on plink formatted phased genotype data?
ThreadText: # How to calculate switch errors on plink formatted phased genotype data?
  
  (Asked by: username_0 on 2022-03-03)
  
  everyone!
  
  I'm working with haplotype inference algorithms in pedigree genotype data, and I would like to know if there is a tool or script to calculate switch errors on phased pedigree data (Plink formatted)?
  
  I already know that VCFtools and other scripts do exist, but they only work with VCF format.
  
  Note: I tried to convert my phased pedigree data to VCF but I lost phase, so, this approach does not seem to be helpful, that's why I'm looking for a specific tool to detect switches on phased pedigree data.
  
  A switch errors ocurr when heterozygous positions are misassigned relative to the previous heterozygous position.
  
  See visual example (block 2), True haplotypes up, inferred haplotypes bottom:
  <https://www.researchgate.net/publication/310766263/figure/fig13/AS:431688409980932@1479933945501/Illustration-of-switch-errors-and-block-breakpoints-In-haplotype-block-2-there-are-two.png>
  
  In my case, I got the phased pedigree plink file as follows:
  
  Infered Haplotype, individual 1:
  1|2 2|1 1|2 1|2 1|2
  
  Real Haplotype, individual 1:
  1|2 1|2 2|1 1|2 1|2
  
  We can see 2 switches, between position 1-2 and 3-4.
  
  Thank you very much in advance!
  Regards!
  
  **Tags:** errors, haplotypes, phasing, pedigree
  
  > **Comments:**
  > **username_1**: Can you explain what switch errors are?  
  > **username_0**: A switch errors occur when heterozygous positions are misassigned relative to the previous heterozygous position.   See visual example (block 2), True haplotypes up, inferred haplotypes bottom: https://www.researchgate.net/publication/310766263/figure/fig13/AS:431688409980932@1479933945501/Illustration-of-switch-errors-and-block-breakpoints-In-haplotype-block-2-there-are-two.png  I got the phased pedigree plink file as follows:  Inferred Haplotype, individual 1: 1 1|2 2|1 1|2 1|2 1|2  Real Haplotype, individual 1: 1 1|2 1|2 2|1 1|2 1|2  See 2 switches, between pos. 1-2 and 3-4.  
  
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  ## 0 answers
  
  