<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>

CC BY-SA 4.0
2022-03-07T14:43:29.120Z
Can you explain what switch errors are?
Dan Bolser
CC BY-SA 4.0
2022-03-08T18:13:12.080Z
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.
Roa.tar
<errors><haplotypes><phasing><pedigree>
How to calculate switch errors on plink formatted phased genotype data?
# 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.  

---

## 0 answers

