I want to use a software for detecting signals of positive selection using genome-wide SNP data. As input data I need the ancestral and derived state for each SNP present in my data.
I found this FAQ http://www.ncbi.nlm.nih.gov/books/NBK44409/#Build.how_do_i_determine_if_a_snp_is_an which points to a file which has the ancestral state for over 60 million SNPs.
I found almost all my SNPs present on that file, but when I was checking the ancestral alleles I encountered two problems:
First, some ancestral alleles didn't match my file. For example in my data SNP 21 rs17003832 22619035 C A, is either C or A. But the ancestral data file points to rs17003832 which has a T.
Second some alleles in the ancestral data file had two SNPs reported as ancestral, for example:
So what should I do? Maybe the first problem could be solved by a strand flip but what about the second one?
Any help would be greatly appreciated.