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

tralalala

YRI, CEU, Sardinian, WestGreenland, CHB, JPT, Sindhi, Papuan, Chukchi, Karitiana

Preset reference populations can be altered. To alter the reference populations one need to write comma separated populations to argument refpops.

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.

The example below show how to make a beagle file of genotype likelihood using ANGSD.

HOME$ ./angsd0.594/angsd -i 'pathtoindi.bam' -GL 2 -sites 'SNP_sites.txt' -doGlf 2 -doMajorMinor 3 -minMapQ 30 -minQ 20 -doDepth 1 -doCounts 1 -out indi_genotypelikelihood

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
...