I am posting this question to BioStars community as I am trying to get a consensus on phasing softwares such as ShapeIT and IMPUTE2, Beagle etc. and their use and application on parasites genomic data (species that are diploid).
For a recent experiment I wanted to use fineStructure to capture the population structure of a parasite population I was studying. fineStructure makes inferences on a population structure based on haplotypes. Therefore input data for fineStructure needs to be phased (phasing infers haplotypes).
I used ShapeIT to phase my parasite genomes and run fineStructure and produced, what I thought was, very informative data.
But alas, upon presenting to the lab my mentor had many reservations, ultimately his reservations were in the phasing software.
Most of these softwares are designed and used on human genomic data, typically from hapmap or 1000 genome were humans are the model organism. Therefore do these software properly phase genomic data from other organisms such as unicellular diploid parasites? or even other mammalian species?
Are there any thoughts or suggestions? How do you know the quality of a phased output data? are these phasing programs too biased to be used on other organisms?
Thank you I hope this makes sense!!!