I downloaded the accompanying snps from the paper:
Genome-wide identification of splicing QTLs in the human brain and their enrichment among schizophrenia-associated loci Atsushi Takata, Naomichi Matsumoto & Tadafumi Kato
but found some strange alignment to the reference genome a small number of the 8966 snps. An example is:
snp pos ref alt chr11 66329732 G A/G
whereas I make this reference base to be A on hg19.
I am not sure what is going on here, and was wondering if I am missing a convention with how these snps are report so I can get the correct alignment. Is it that 'ref' is not actually the reference base, but the allele with higher frequency? Given this isn't reported in the paper it makes it quite tricky to ensure the correct alignment of snps to the reference genome.