ANGSD: Analysis of next generation Sequencing Data

Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.


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To estimate admixture proportions from sequencing data then you can use NGSadmix

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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