I'm pretty new to GWAS so I'm still figuring out all the programs to use and how, and I have some questions.
My situation is that I have a bunch of individual fish that I want to do GWAS with, and I am using quantitative data as the phenotype and RAD sequencing data. I have used PLINK to do SNP by SNP associations but now I want to use phased and imputed data. I have used fastphase to phase the data and impute missing genotypes but now I want to use these data to do an association with my phenotypes. From my understanding PLINK does not handle phased data that has been phased outside of it's program (and I would like to use another program anyway because PLINK doesn't handle scaffolds well). I am wondering what people do with their data after they run it through fastphase. Can I just convert file formats to run it in SNPTEST? Will this work? Do I need to instead phase my data in IMPUTE2 and then move it to SNPTEST? Is there another good association testing program aside from SNPTEST and PLINK that will work with the fastphase file output?
I have read about a lot of people using fastphase, but I haven't seen any examples of people using an association program after fastphasing their data.
Any help would be very much appreciated.