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Using admixture to estimate ancestry from a single VCF with no family information

Hello,

I'm trying to use admixture to estimate ancestry from a single VCF, following the manual from https://dalexander.github.io/admixture/admixture-manual.pdf

  1. I first create a plink .ped file with vcftools. I then have a .ped and a .map file.

  2. I run admixture thus:

    /home/con/Downloads/dist/admixture_linux-1.3.0/admixture ZZFNMDMF.ped 1

and get the output:

****                   ADMIXTURE Version 1.3.0                  ****
****                    Copyright 2008-2015                     ****
****           David Alexander, Suyash Shringarpure,            ****
****                John  Novembre, Ken Lange                   ****
****                                                            ****
****                 Please cite our paper!                     ****
****   Information at www.genetics.ucla.edu/software/admixture  ****

Random seed: 43
Point estimation method: Block relaxation algorithm
Convergence acceleration algorithm: QuasiNewton, 3 secant conditions
Point estimation will terminate when objective function delta < 0.0001
Estimation of standard errors disabled; will compute point estimates only.
PLINK Input file error

The error PLINK Input file error tells me absolutely nothing about what the error is.

A similar error is here on BioStars but there is no solution: Admixture give me an error with ped "PLINK Input file error" and with bed format quit with error message "Abort trap6

How can I use admixture? or is there easier/less bug-prone software available?

admixture
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updated by 4galaxy77 4galaxy77 • written by dec986 dec986

Does your sample only have one individual?

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written by 4galaxy77 4galaxy77

yes, there is only 1 sample

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written by dec986 dec986

Well there's no way to use admixture if you only have a single individual. If you are estimating ethnicity, you need to download a reference panel like the 1000 genomes and run it in supervised mode.

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written by 4galaxy77 4galaxy77

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