NGSadmix

To estimate admixture proportions from sequencing data then you can use NGSadmix NGSadmix has it's very own webpage, because we like it so much. NGSadmix webpage

Quick run

You can generate input files for NGSadmix easily in ANGSD see Beagle_input.

./angsd -GL 1 -out genolike -nThreads 10 -doGlf 2 -doMajorMinor 1 -SNP_pval 1e-6 -doMaf 1  -bam bam.filelist

and then run NGSadmix (found in the mics folder in the angsd folder)

NGSadmix -likes input.gz -K 3 -P 4 -o myoutfiles -minMaf 0.05