Comments (5)
Dsuite outputs all combinations of populations, not all permutations. With three populations, you have one trio.
If, for some reason, you want all permutations of your three populations, you can specify the different arrangements using the --tree option. Still, there are only three arrangements meaningfully calculate:
((P1,P2),P3); ((P1,P3),P2); ((P2,P3),P1)
This is because the rest are just the mirror image: ((P1,P2),P3) is the mirror image of ((P2,P1),P3). The D statistics will be exactly the same, just the sign reversed (i.e. one positive and the other negative).
Milan
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In the beginning I had the same problem as you. you can seach the answer in the close issues#35.
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In the beginning I had the same problem as you. you can seach the answer in the close issues#35.
Hi,Could you share how you deal with it? Now I got P1=A, P2=B, P3=C, but I want a setting P1=B, P2=A, P3=C, and get Dstatistic and Z-score, could you share your solutions? Thanks!
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I thought, for example, P1=A, P2=B, P3=C, Dstatistic=0.01, Z=10, p=0, then based on the formula in the Dsuite paper, when P1=B, P2=A, P3=C, the Dstatistic should be -0.01, Z = D/std_err(D), the Z result should be -10, and P value should be 1-P_original=1-0=1. Thanks
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Related Issues (20)
- Different results obtained when using Dtrios and DParallel on the same vcf file
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- make a release or tag versions ?
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- The sample is in the VCF but not assigned in the SETS.txt HOT 8
- Question about order of population set when running Dtrios HOT 1
- Only plot fbranch results with Z>=3 HOT 1
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- non-significant D-statistic with significant clustering (homoplasy test) HOT 2
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- Dinvestigate issue: D.cpp:80: void doAbbaBaba(): Assertion `threePops.size() == 3' failed HOT 2
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