18. Estimation of Individual Ancestries

Based on Dataset II, we perform an Analysis of Estimation of Individual Ancestries.

Runs ngsAdmix--v32 on the .beagle file using the wrapper_ngsAdmix:

export N_REP=100

for K in `seq -w 2 25`
do 
    echo $SCRIPTS/scripts/wrapper_ngsAdmix.sh -P 15 -debug 1 -likes ~/data/Pigeons/PBGP/PBGP--Analyses/PBGP--ANGSDRuns/PBGP--GoodSamples_WithWGSs_NoCrupestris_SNPCalling--Article--Ultra.beagle.gz -K $K -minMaf 0 -tol 1e-6 -tolLike50 1e-3 -maxiter 10000 -o ~/data/Pigeons/PBGP/PBGP--Analyses/PBGP--ngsAdmix/PBGP--GoodSamples_WithWGSs_NoCrupestris_SNPCalling--Article--Ultra.${K}

done | xsbatch -c 15 --mem-per-cpu 256 -J ngsAdmix -R --time 10-00 --

These ngsAdmix results were plotted using the Rscript below (.annot file as in 14.):

• PBG--ngsAdmix.R

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