ANGSD: Analysis of next generation Sequencing Data
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NGSadmix: Difference between revisions
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To estimate admixture proportions from sequencing data then you can use NGSadmix | 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) | |||
<pre> | |||
NGSadmix -likes input.gz -K 3 -P 4 -o myoutfiles -minMaf 0.05 | |||
</pre> | |||
Latest revision as of 16:44, 7 February 2018
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