Hi, I downloaded ENCODE genotype calls from UCSC table browser. The genotypes were obtained with the Illumina 1M-Duo. But they come in the AA/AB/BB format.
I have been trying to understand how to convert them to A,C,G,T... I guess there should be an allele table that would tell me what is the A and B allele for each SNP?
This is the file I downloaded: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeHaibGenotype/supplemental/wgEncodeHaibGenotypeGtypeSnp.txt