Does any one know on what base does PharmGKB decide haplotype reference allele?. I checked different snps in dbsnp the reference alleles are not same in Pharmgkb haplotype table and that of dbsnp like rs3818247
reference allele in dbsnp is G but in PharmGKB haplotype table of HNF4A reference allele is T
I would try to avoid thinking along the lines of reference / alternate (REF / ALT) bases when using PharmGKB data. The data in PharmGKB is curated from published literature and just lists the known genotype of each haplotype. These genotypes may or may not be the reference base in a given reference genome build. The only thing that you need to know, however, is the exact bases that form the haplotypes.
Note that a rs ID from dbSNP should neither be thought along the lines of REF / ALT and should more be regarded in the sense that a particular rs ID relates to a position in the genome whose genotype varies among individuals. For all intents and purposes, REF / ALT is meaningless and even the 'reference' base may be pathogenic. Please, read my answer here to be enlightened, in this regard: A: Alternate nucleotide is more frequent than reference nucleotide. OMG I'm dizzy.
Here is the haplotype table for HNF4A from PharmGKB:
All you need to worry about are those bases listed for each haplotype, irrespective of whether they are the REF or ALT in a given reference genome. Thus, when processing your own data and matching to these haplotype tables, you simply need to know the base at each relevant position in your sample. Technically, you don't even need to use a variant caller.