Processing data from genotyping chips

1. A system for processing genetic data, including:

a processor configured to:

receive two or more genetic data sets for an individual from one or more genetic data sources, wherein the genetic data sets comprises information pertaining to the individual's deoxyribonucleic acid (DNA) data;

merge the genetic data sets from the one or more genetic data sources to obtain a set of merged genetic data for the individual, including to:

identify a single nucleotide polymorphism (SNP) that is a duplicate SNP of the genetic data sets, wherein the SNP is associated with a variation that occurs at a location in the individual's DNA sequence, and values corresponding to the duplicate SNP in the genetic data sets are different;

analyze the values of the duplicate SNP to resolve a discrepancy attributed to different values corresponding to the duplicate SNP and automatically determine an appropriate value that corresponds to the duplicate SNP, the analysis and determination being based at least in part on contextual information; and

store the set of merged genetic data for the individual; wherein

the appropriate value that is determined is stored in the set of merged genetic data, and a different value that corresponds to the duplicate SNP is not stored in the set of merged genetic data; and

a memory coupled to the processor and configured to provide the processor with instructions.

2. The system of claim 1 , wherein to store the set of merged genetic data includes to create a data structure for the individual's data.

3. The system of claim 2 , wherein the data structure includes information relevant to a specific application.

4. The system of claim 2 , wherein to store the set of merged genetic data includes to store the data structure in a database that can be accessed by an application for analyzing DNA data.

5. The system of claim 4 , wherein the application for analyzing DNA data includes a website.

6. The system of claim 1 , wherein to receive two or more genetic data sets for an individual includes to create a data structure for each genetic data set and store the data for each genetic data set in a data structure.

7. The system of claim 1 , wherein to merge the genetic data sets from the one or more genetic data sources includes to create a first data structure for storing the individual's merged genetic data; and a second data structure for storing a more limited set of the individual's data.

8. The system of claim 1 , wherein to store the set of merged genetic data for the individual includes to store the data in a particular order or location that is the same for every individual.

9. The system of claim 1 , wherein the two or more data sets include an intensity value, a genotype call, or a confidence value associated with a genotype call.

10. The system of claim 1 , wherein the set of merged data is stored in a structure having a plurality of entries each corresponding to a SNP.

11. The system of claim 1 , wherein the contextual information includes linkage disequilibrium information.

12. The system of claim 1 , wherein the genetic data source includes a genotyping chip or platform.

13. The system of claim 1 , wherein the contextual information includes family inheritance information.

14. The system of claim 1 , wherein the contextual information includes population-specific information.

15. The system of claim 11 , wherein a lookup table is provided for mapping each of the plurality of entries to a chromosome positional index.

16. The system of claim 1 , wherein the contextual information includes information pertaining to the SNP that was assayed by multiple probes.

17. The system of claim 1 wherein duplicate SNP to select a value to be stored for the duplicate SNP comprises adjusting a prior probability.

18. The system of claim 1 wherein duplicate SNP to select a value to be stored for the duplicate SNP comprises adjusting an observed probability.

19. A method for processing genetic data, including:

receiving two or more genetic data sets for an individual from one or more genetic data sources, wherein the genetic data sets comprises information pertaining to the individual's deoxyribonucleic acid (DNA) data;

merging the genetic data sets from the one or more genetic data sources to obtain a set of merged genetic data for the individual, including:

identifying a single nucleotide polymorphism (SNP) that is a duplicate SNP of the genetic data sets, wherein the SNP is associated with a variation that occurs at a location in the individual's DNA sequence, and values corresponding to the duplicate SNP in the genetic data sets are different;

analyzing the values of the duplicate SNP to resolve a discrepancy attributed to different values corresponding to the duplicate SNP and automatically determining an appropriate value that corresponds to the duplicate SNP, the analysis and determination being based at least in part on contextual information; and

storing the set of merged genetic data for the individual; wherein

the appropriate value that is determined is stored in the set of merged genetic data, and a different value that corresponds to the duplicate SNP is not stored in the set of merged genetic data.

20. A computer program product for processing genetic data, the computer program product being embodied in a computer readable medium and comprising computer instructions for:

receiving two or more genetic data sets for an individual from one or more genetic data sources, wherein the genetic data sets comprises information pertaining to the individual's deoxyribonucleic acid (DNA) data;

merging the genetic data sets from the one or more genetic data sources to obtain a set of merged genetic data for the individual, including:

identifying a single nucleotide polymorphism (SNP) that is a duplicate SNP of the genetic data sets, wherein the SNP is associated with a variation that occurs at a location in the individual's DNA sequence, and values corresponding to the duplicate SNP in the genetic data sets are different;

analyzing the values of the duplicate SNP to resolve a discrepancy attributed to different values corresponding to the duplicate SNP and automatically determining an appropriate value that corresponds to the duplicate SNP, the analysis and determination being based at least in part on contextual information; and

storing the set of merged genetic data for the individual; wherein

the appropriate value that is determined is stored in the set of merged genetic data, and a different value that corresponds to the duplicate SNP is not stored in the set of merged genetic data.