Strand Flip

[Rocio Mariana]

Hi,

I hope you can help me with a last issue that I have with a Quality Control that I'm doing. 

I want to check if I have to flip the strand of SNP from a file that is a merge. 

So I first use snpflip, because it gives me two files, one of ambiguous snps and one with those that I have to flip. This analysis gave me a file with 39,513 SNPs that I have to flip. 

Then I used --flip-scan option of plink1.9 and gave me a file with 2317 SNPs and I have to flip.

I found that snpflip is the best choise, but it seems weird the huge difference between both analisys.

Thanks, 

[Christopher Chang]

—flip-scan is just for resolving ambiguous A/T and C/G SNPs.