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HOME$ Rscript NGS_Admix_rscript.r beagle_GL='indi_genotypelikelihood.beagle' popfreq_RDATA='pop_freq_all.RData' outputfile='test' | HOME$ Rscript NGS_Admix_rscript.r beagle_GL='indi_genotypelikelihood.beagle' \n popfreq_RDATA='pop_freq_all.RData' outputfile='test' | ||
</pre> | </pre> | ||
=Input Files= | =Input Files= | ||
Revision as of 20:18, 21 September 2014
This page contains information about the program called FastNGSadmix, which is a very fast tool for finding admixture proportions from NGS data of a single individual. It is based on genotype likelihoods. The program is written in R.
Installation
wget popgen.dk/?? OR Use shiny: popgen.dk/???
Run example
First download some example test files which has been generated on basis of data from the 1000 genomes project.
wget popgen.dk/??????/popfreq.RData wget popgen.dk/??????
HOME$ Rscript NGS_Admix_rscript.r beagle_GL='indi_genotypelikelihood.beagle' \n popfreq_RDATA='pop_freq_all.RData' outputfile='test'