Hi, I am new using SHAPEIT and I have a problem after running it.
I am using the last version and I used the following: shapeit -B chr1 -M genetic_map_chr1_combined_b37.txt -O chr1.phased
and I got this error (it run for about 1 hour): [33mERROR:[0m 313 samples are included in several duos/trios, check list in shapeit_31082017_16h30m20s_99999c8b-ee39-4407-9ce8-3b1842735b04.inc.me You can use the --duohmm flag to phase complex pedigrees.
I tried to use the --duohmm flag but it is still running for about 80 hours. I really do not know if it will solve the problem. I know I have some families with more than 1 children or father that have 2 children with 2 different wives. I think this is th reason why this error appear. After I want to use the RFMIX program for local admixture.
Did someone use SHAPEIT and had the same problem? How did you solve it?
Thank you very much!!!