Question: MACH imputation result QC
1
gravatar for Zhenyu Zhang
5.3 years ago by
Zhenyu Zhang260
United States
Zhenyu Zhang260 wrote:

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.

snp qc mach rsq imputation • 2.6k views
ADD COMMENTlink written 5.3 years ago by Zhenyu Zhang260
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