FastNgsAdmixOld

This page contains information about the program called FastNGSadmixPCA, which is a very fast tool for finding admixture proportions from NGS data of a single individual to incorporate into PCA of NGS data. It is based on genotype likelihoods. The program is written in R.

Installation

wget http://popgen.dk/albrecht/kristian/tool_download.zip
unzip tool_download.zip
OR simply use SHINY:
http://popgen.dk:443/kristian/admixpca_human/

Run example

tool.zip contains all files needed to execute FASTNGSAdmixPCA. The sample is from the HAPMAP project. In need of more samples, one can find a couple more samples in http://popgen.dk/albrecht/kristian/ The Rscript below executes the tool. all output is directed to a output_folder that is created in the process. To see the preset: Rscript FastNGSAdmixPCA.r

Rscript FastNGSAdmixPCA.r infile=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz

All arguments can be altered. To alter the reference populations, one need to write comma separated populations to the refpops argument as shown below

Rscript FastNGSAdmixPCA.r infile=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz refpops=YRI,JPT,CHB,CEU

To get an overview of available reference populations, one can make a dry run

Rscript FastNGSAdmixPCA.r infile=TRUE dryrun=TRUE

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' -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
...

version 2

This program needs the genotype likelihoods in the beagle file format. It also needs frequencies of a reference panel with the populations for which admixture proportions should be estimated, for instance from 1000 G or HGDP, or a custom made reference panel, it should be noted that the frequencies in the reference panel should be of the major allele in the beagle file.

(So if the 3 columns with genotype likelihoods in the beagle file is coded like this AA AB BB, then the frequencies should be of the A allele.)

Furthermore a file with the number of individuals in each reference population should be supplied.

An example of a command:

./fastNGSadmix -likes Yoruba10Japanese65Han25_3000000_d10_N10_GL.txt -fname Yoruba10Japanese65Han25_3000000_d10_N10_Ref.txt -Nname sYoruba10Japanese65Han25_3000000_d10_N10_nInd.txt -outfiles Yoruba10Japanese65Han25_3000000_d10_N10

Then a lot of different options and filters can be specified:

(TO BE CONTINUED...)