SHAPEIT error after run: x samples are included in several duos/trios
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3.9 years ago

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!!!

shapeit phasing inferring haplotypes snp • 1.3k views
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2.8 years ago
chariko ▴ 50

did you manage to solve your problem?

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