FastNgsAdmixOld

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/??????/beagle.gz

refpops = c('YRI','CEU','Sardinian','WestGreenland','CHB','JPT',
  'Sindhi','Papuan','Chukchi','Karitiana')
<\pre>

Preset reference populations can be altered.

<pre>
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
...