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Question: Error while running Admixture program with .bed files
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gravatar for always_learning
6.3 years ago by
always_learning • 1.0k
Doha, Qatar
always_learning • 1.0k wrote:

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
admixture • 4.1k views
ADD COMMENT • link •
modified 6.3 years ago by chrchang523 ♦ 7.3k • written 6.3 years ago by always_learning • 1.0k
2
gravatar for chrchang523
6.3 years ago by
chrchang523 ♦ 7.3k
United States
chrchang523 ♦ 7.3k wrote:

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.
ADD COMMENT • link written 6.3 years ago by chrchang523 ♦ 7.3k
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