Ancestry painting with local ancestry inference

1. A computer-implemented method for graphically displaying ancestry composition information using a user interface, the method comprising:

receiving, from a user via the user interface, a request to display ancestry composition information for an individual;

obtaining ancestry composition information comprising proportions of the individual's genotype data deemed to correspond to specific ancestries; and

displaying, via the user interface, ancestry composition information of the individual in a circular representation, wherein the circle comprises a plurality of sections, each section sized to represent a portion of the individual's genotype corresponding to a specific ancestry.

2. The method of claim 1 , wherein the plurality of sections are presented in different visual formats to represent different specific ancestries.

3. The method of claim 2 , wherein the visual formats comprise different colors and/or patterns.

4. The method of claim 2 , further comprising displaying a list of the specific ancestries and their proportions of the individual's genotype corresponding to the specific ancestries.

5. The method of claim 2 , further comprising displaying a map of the specific ancestries of the individual's genotype.

6. The method of claim 1 , wherein the specific ancestries of the individual's genotype data represent geographical regions.

7. The method of claim 6 , wherein the geographic regions comprise continents.

8. The method of claim 1 , wherein the ancestry composition information includes hierarchical information of different geographical regions.

9. The method of claim 1 , further comprising:

receiving, from the user via the user interface, a request to display ancestry composition information for subregions of a first specific ancestry, and

displaying, via the user interface, the ancestry composition information of the individual by subregions of the first specific ancestry.

10. The method of claim 9 , wherein the request to display ancestry composition information for subregions of a first specific ancestry comprises input caused by the user moving a cursor over the subregions displayed via the user interface.

11. The method of claim 9 , wherein the request to display ancestry composition information for subregions of a first specific ancestry comprises input caused by the user clicking on the subregions displayed via the user interface.

12. The method of claim 9 , wherein the ancestry composition information of subregions is presented in a plurality of subportions, each sized to represent a proportion of the individual's genotype corresponding a specific subregion.

13. The method of claim 9 , wherein displaying the ancestry composition information of the individual by subregions of the first specific ancestry comprises expanding a first section of the circular representation for the first specific ancestry.

14. The method of claim 13 , wherein expanding the first section of the circular representation shows the subregions of the first specific ancestry.

15. The method of claim 13 , further comprising:

receiving, from the user via the user interface, a request to expand a first subregion of the first specific ancestry,

displaying, via the user interface, the ancestry composition information for a more specific geographic location within the first subregion.

16. The method of claim 9 , wherein displaying the ancestry composition information of the individual by subregions of the first specific ancestry comprises displaying additional sections indicating geographic regions within a continent corresponding to the first specific ancestry.

17. The method of claim 1 , further comprising:

receiving, from the user via the user interface, a request to display ancestry composition inherited from one or both parents; and

displaying, via the user interface, the ancestry composition information of the individual inherited from the one or both parents.

18. The method of claim 1 , wherein the ancestry composition information includes inheritance information comprising proportions of the individual's ancestries inherited from each parent of the individual.

19. The method of claim 1 , further comprising:

receiving, from the user via the user interface, a request to display the ancestry composition information for a specific chromosome; and

displaying, via the user interface, the ancestry composition information of the individual for the specific chromosome.

20. The method of claim 1 , wherein the genotype data for the ancestry composition information is from autosomal chromosomes.

21. The method of claim 1 , wherein displaying, via the user interface, the ancestry composition information of the individual comprises displaying specific continents to which the individual's genotype data corresponds.

22. The method of claim 1 , wherein obtaining ancestry composition information of the individual comprises receiving the ancestry composition information from a database or a pipelined ancestry prediction process.

23. The method of claim 22 , wherein the pipelined ancestry prediction process comprises:

obtaining unphased genotype data of the individual;

phasing the unphased genotype data to generate phased haplotype data; and

using a machine learning trained model to classify portions of the phased haplotype data as corresponding to specific ancestries and generate the ancestry composition information.

24. The method of claim 22 , wherein the pipelined ancestry prediction process comprises

recalibrating posterior probabilities that a proportion of the individual's genotype data corresponds to a specific ancestry and generating the ancestry composition information.

25. The method of claim 22 , wherein the pipelined ancestry prediction process comprises clustering posterior probabilities that proportions of the individual's genotype data correspond to specific ancestries until the clustered posterior probability meets or exceeds a threshold value.

26. The method of claim 25 , wherein the clustering is performed by adding the posterior probability of specific ancestries associated with a geographical hierarchy.

27. The method of claim 1 , wherein the ancestry composition information is obtained per haplotype segment.

28. The method of claim 27 , further comprising tallying the ancestry composition information from a plurality of haplotype segments.