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.
NGSadmix
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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