Our standard AF values are allele frequencies rounded to two decimal places calculated using allele count (AC) and allele number (AN) values.
LDAF is an allele frequency value in the info column of our phase 1 VCF files. LDAF is the allele frequency as inferred from the haplotype estimation. You will note that LDAF does sometimes differ from the AF calculated on the basis of allele count and allele number. This generally means there are many uncertain genotypes for this site. This is particularly true close to the ends of the chromosomes.
The phase 1 data set also contains Genotype Dosage values. This comes from Mach/Thunder, imputation engine used for genotype refinement in the phase 1 data set.
The Dosage represents the predicted dosage of the non reference allele given the data available, it will always have a value between 0 and 2.
The formula is Dosage = Pr(Het|Data) + 2*Pr(Alt|Data)
The dosage value gives an indication of how well the genotype is supported by the imputation engine. The genotype likelihood gives an indication of how well the genotype is supported by the sequence data.
There are a small number of variants which have an Allele Count of 0 and an Allele Frequency of 0.
This is because the original sample list for phase1 had 1094 samples on it. After our integrated genotyping processes 2 samples where discovered to have very discordant genotypes.
The decision was made to leave in any variant which only been discovered in one or both of these individuals. The Analysis group is still confident in their sites but not in their genotypes. In doing this we are left with some variant sites where no sample holds the non reference allele.