ANGSD: Analysis of next generation Sequencing Data

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To estimate admixture proportions from sequencing data then you can use NGSadmix [[File:admixtureNGS.png|thumb]]
NGSadmix has it's very own webpage, because we like it so much.
NGSadmix has it's very own webpage, because we like it so much.
[http://www.popgen.dk/software/index.php/NgsAdmix NGSadmix webpage]


http://www.popgen.dk/software/index.php/NgsAdmix
===Quick run===
You can generate input files for NGSadmix easily in ANGSD see [[Beagle_input]].
<pre>
./angsd -GL 1 -out genolike -nThreads 10 -doGlf 2 -doMajorMinor 1 -SNP_pval 1e-6 -doMaf 1  -bam bam.filelist
</pre>


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


You can generate input files for NGSadmix easily in ANGSD see [[Beagle_input]].
<pre>
NGSadmix -likes input.gz -K 3 -P 4 -o myoutfiles -minMaf 0.05
</pre>

Latest revision as of 15:44, 7 February 2018

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

Error creating thumbnail: File missing

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