I would like to get the r-squared for two SNPs in my population. One of the SNPs is in a mySQL db, and the other is currently also in a mySQL db, but I have the plink files for that one.
Can anyone advise me on how I will go about getting these into a format that Haploview will understand?
EDIT:
Just to clarify, I've two SNPs from different data sources on the patients. While they are indicated to be perfect proxies for each other (1000Genomes), they present different p-values when the Jonckheere-Tempstra test is performed, SNP-A (p=0.2192), SNP-B (p=0.0152). I've been asked to get the r-square between them.
Haploview accepts a plink format, I don't have the plink files for SNP-A, that is contained entirely within a mySQLdb, converted over from the SAS format of a previous student. I do have the plink files for SNP-B, but it is split into two separate plink datasets. Both datasets can be merged using plink, but there is still the issue of SNP-A not being available in a plink format.
To clarify, do the samples overlap for these 2 SNPs?
Yes, ~97% of them.
Someone mentioned to me that I could output each of the SNPs into an excel file, and do it from there. Then I would need a file with the pair of genotypes at each locus listed for each person. I'm actually a computer scientist, I've never used this tool before. Are we talking two columns, with each row a patient, and each column a SNP?