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!
