For eqtl analysis, I used mach admix to imputed SNP6 array data against 1000G. Then the next step which got me confused is which SNP to keep:
There are a lot output files provided by mach, including qc.gz file, some Rsq and Quality scores in out.info file. What I did is filter out Rsq<0.3, and use the dose of each SNP.
Did I miss some other important quality information? Especially someone mentioned "information content scores" to me, which I couldn't find in these output. Thanks.