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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!

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  • $\begingroup$ Can you explain what switch errors are? $\endgroup$
    – Dan Bolser
    Mar 7, 2022 at 14:43
  • $\begingroup$ 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: researchgate.net/publication/310766263/figure/fig13/… 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. $\endgroup$
    – Roa.tar
    Mar 8, 2022 at 18:13

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