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?
It can be a bit messy, get SNP names from plink MAP file, get strands and alleles from UCSC Tables, check if alleles match, then add strands, then flip. Or download SNP file from illumina to get strands?
No, it is very easy. Please see: https://github.com/endrebak/snp-flip
REPO NOW AT https://github.com/endrebak/snpflip