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=Input Files= | =Input Files= | ||
Input files are contains genotype likelihoods in genotype likelihood beagle input file format [http://faculty.washington.edu/browning/beagle/beagle.html]. We recommend [ANGSD] for easy transformation of Next-generation sequencing data to beagle format. | |||
Example of a beagle genotype likelihood input file for 3 individuals. | |||
<pre> | |||
marker allele1 allele2 Ind0 Ind0 Ind0 | |||
1_14000023 1 0 0.941 0.058 0.000 | |||
1_14000072 2 3 0.709 0.177 0.112 | |||
1_14000113 0 2 0.855 0.106 0.037 | |||
1_14000202 2 0 0.835 0.104 0.060 | |||
... | |||
</pre> | |||
Revision as of 20:59, 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' popfreq_RDATA='pop_freq_all.RData' outputfile='test'
Input Files
Input files are contains genotype likelihoods in genotype likelihood beagle input file format [1]. We recommend [ANGSD] for easy transformation of Next-generation sequencing data to beagle format.
Example of a beagle genotype likelihood input file for 3 individuals.
marker allele1 allele2 Ind0 Ind0 Ind0 1_14000023 1 0 0.941 0.058 0.000 1_14000072 2 3 0.709 0.177 0.112 1_14000113 0 2 0.855 0.106 0.037 1_14000202 2 0 0.835 0.104 0.060 ...