Hello,
I have both sequencing and genotype data for a small population and was wondering how to go about analyzing whether any of these individuals have a shared haplotypes along a particular chromosome.
I phased my data with SHAPEIT, but I'm having trouble analyzing whether any individuals share a haplotype.
If anyone has any experience in this regard or in interpreting SHAPEIT output files, please post a response.
Thank you.
Hi Ricky
I have not experience with SHAPEIT, but it is rather easy to get a list of haplotype frequencies with package haplo.stats, which works with R statistical package.Shared haplotypes are those with absolute frequencies above 1.
Here you can find a Tutorial on how to use it
http://faculty.washington.edu/kenrice/sisg/haplo.stat.pdf
Hope this helps
Pablo
Hi Ricky,
To analyze haplotypes you can use DNAsp software (Rozas et al., 2009). See link: http://www.ub.edu/dnasp/
To analyze genotypes depends on your data, if you have microsatellites you can use micro-satellite toolkit, is a package of excel, I can share you the zip file.
I hope this helps
Cheers
Nancy
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