I have GWAS data from Illumina HumanOmniExpress BeadChip in PLINK format. I am wondering the easiest way to find SNPs not mapped to the positive strand (using reference hg19/b37) and flip them. I know PLINK has the --flip command but it needs a list of SNPs to flip. How do I generate this list?
I wrote a command line tool to do this very thing. Please see https://github.com/endrebak/snp-flip
The tool works right out of the box as long as you have biopython installed and a reference genome to do lookups in. See the github repo README.md for examples and documentation. It comes with example files to play around with.
You should look in the original output file (finalreport). This file sould have Top alleles (Illumina nomenclature) and the forward alleles. If you do the flip by comparing your minor allele with those from UCSC, all SNPs with MAF around 45% are problematic, especially AT and CG SNPs.