Error while running Admixture program with .bed files

Question

[always_learning]

Hello All,

I was trying to run Admixture with around 140 population but getting errors like:

Error: detected that all genotypes are missing for a SNP locus.
Please apply quality-control filters to remove such loci

If some one else faced similar error with Admixture and if yes then what was work around ?

 

Thanks

Syed

Answer 1

[chrchang523]

plink --bfile [filename prefix] --geno 0.999 --make-bed --out [new prefix]

is a quick way to remove all loci where more than 99.9% of genotypes are missing.

It sounds like this is a raw dataset that requires more preprocessing, though; in particular, something like --indep-pairwise should be used.  See the Admixture manual (https://www.genetics.ucla.edu/software/admixture/admixture-manual.pdf ) for a bit of discussion.