Hi, can you post an example of what your file currently gives you? I suspect you are getting phased output from tped, whereas gen.txt is not phased but the unphased genotype, so you would add together phased output in the obvious way to get unphased genotype. I can offer suggestions on this if you post part of an example. Note that gen.txt is optional, you don’t need it to run STITCH, it is just helpful to show accuracy as you progress through the EM algorithm

[yao-chenxin]

Hi, can you post an example of what your file currently gives you? I suspect you are getting phased output from tped, whereas gen.txt is not phased but the unphased genotype, so you would add together phased output in the obvious way to get unphased genotype. I can offer suggestions on this if you post part of an example. Note that gen.txt is optional, you don’t need it to run STITCH, it is just helpful to show accuracy as you progress through the EM algorithm

Originally posted by @rwdavies in #51 (comment)