software - User contributions [en]

FastNgsAdmixOld

2014-10-17T09:32:31Z

Kehanghoej:

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 OCA of NGS data. It is based on genotype likelihoods. The program is written in R.

=Installation=
<pre>
wget http://popgen.dk/albrecht/kristian/tool_download.zip
unzip tool_download.zip
OR simply use SHINY:
http://popgen.dk:443/kristian/admixpca_human/
</pre>

=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
<pre>
Rscript FastNGSAdmixPCA.r infile=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz
</pre>
All arguments can be altered. To alter the reference populations, one need to write comma separated populations to the refpops argument as shown below

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

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

<pre>
Rscript FastNGSAdmixPCA.r infile=TRUE dryrun=TRUE
</pre>

=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.

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

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>

FastNgsAdmixOld

2014-10-15T18:33:46Z

Kehanghoej:

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 OCA of NGS data. It is based on genotype likelihoods. The program is written in R.

=Installation=
<pre>
wget http://popgen.dk/albrecht/kristian/tool_download.zip
unzip tool_download.zip
OR
Use shiny: http://popgen.dk:443/kristian/admixpca_human/
</pre>

=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
<pre>
Rscript FastNGSAdmixPCA.r infile=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz
</pre>
All arguments can be altered. To alter the reference populations, one need to write comma separated populations to the refpops argument as shown below

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

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

<pre>
Rscript FastNGSAdmixPCA.r infile=TRUE dryrun=TRUE
</pre>

=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.

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

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>

FastNgsAdmixOld

2014-10-15T18:33:18Z

Kehanghoej:

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 OCA of NGS data. It is based on genotype likelihoods. The program is written in R.

=Installation=
<pre>
wget http://popgen.dk/albrecht/kristian/tool_download.zip
unzip tool_download.zip
OR
Use shiny: http://popgen.dk:443/kristian/admixpca_human/
</pre>

=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
<pre>
Rscript FastNGSAdmixPCA.r infile=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz
</pre>
All arguments can be altered. To alter the reference populations, one need to write comma separated populations to the refpops argument as shown below

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

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

<pre>
Rscript FastNGSAdmixPCA.r infile=TRUE dryrun=TRUE
</pre>

=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.

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

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>

FastNgsAdmixOld

2014-10-15T18:32:37Z

Kehanghoej:

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 OCA of NGS data. It is based on genotype likelihoods. The program is written in R.

=Installation=
<pre>
wget http://popgen.dk/albrecht/kristian/tool_download.zip
unzip tool_download.zip
OR
Use shiny: http://popgen.dk:443/kristian/admixpca_human/
</pre>

=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
<pre>
Rscript FastNGSAdmixPCA.r infile=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz
</pre>
All arguments can be altered. To alter the reference populations, one need to write comma separated populations to the refpops argument as shown below
<pre>
Rscript FastNGSAdmixPCA.r infile=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz refpops=YRI,JPT,CHB,CEU
</pre>

To get an overview of all reference populations, one can make a dry run
<pre>
Rscript FastNGSAdmixPCA.r infile=TRUE dryrun=TRUE
<\pre>

=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.

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

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>

FastNgsAdmixOld

2014-10-15T18:21:51Z

Kehanghoej:

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 OCA of NGS data. It is based on genotype likelihoods. The program is written in R.

=Installation=
<pre>
wget http://popgen.dk/albrecht/kristian/tool_download.zip
unzip tool_download.zip
OR
Use shiny: http://popgen.dk:443/kristian/admixpca_human/
</pre>

=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
<pre>
Rscript FastNGSAdmixPCA.r infile=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz
</pre>
All arguments can be altered. To alter the reference populations, one need to write comma separated populations to the refpops argument as shown below
<pre>
Rscript FastNGSAdmixPCA.r infile=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz refpops=YRI,JPT,CHB,CEU
</pre>

make a dry run version to get ref pop names only. something false true

=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.

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

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>

FastNgsAdmixOld

2014-10-15T18:20:23Z

Kehanghoej:

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 OCA of NGS data. It is based on genotype likelihoods. The program is written in R.

=Installation=
<pre>
wget http://popgen.dk/albrecht/kristian/tool.zip
unzip tool.zip
OR
Use shiny: http://popgen.dk:443/kristian/admixpca_human/
</pre>

=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
<pre>
Rscript FastNGSAdmixPCA.r infile=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz
</pre>
All arguments can be altered. To alter the reference populations, one need to write comma separated populations to the refpops argument as shown below
<pre>
Rscript FastNGSAdmixPCA.r infile=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz refpops=YRI,JPT,CHB,CEU
</pre>

make a dry run version to get ref pop names only. something false true

=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.

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

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>

FastNgsAdmixOld

2014-10-15T13:30:40Z

Kehanghoej:

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 OCA of NGS data. It is based on genotype likelihoods. The program is written in R.

=Installation=
<pre>
wget http://popgen.dk/albrecht/kristian/Fast_NGS_PCA_refdata/tool.zip
unzip tool.zip
OR
Use shiny: http://popgen.dk:443/kristian/admixpca_human/
</pre>

=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
<pre>
Rscript FastNGSAdmixPCA.r infile=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz
</pre>
All arguments can be altered. To alter the reference populations one need to write comma separated populations to argument ref pops as shown below
<pre>
Rscript FastNGSAdmixPCA.r infile=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz refpops=YRI,JPT,CHB,CEU
</pre>

make a dry run version to get ref pop names only. something false true

=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.

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

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>

FastNgsAdmixOld

2014-10-15T13:30:09Z

Kehanghoej:

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 OCA of NGS data. It is based on genotype likelihoods. The program is written in R.

=Installation=
<pre>
wget http://popgen.dk/albrecht/kristian/Fast_NGS_PCA_refdata/tool.zip
unzip tool.zip
OR
Use shiny: http://popgen.dk:443/kristian/admixpca_human/
</pre>

=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
<pre>
Rscript FastNGSAdmixPCA.r infile=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz
</pre>
All arguments can be altered. To alter the reference populations one need to write comma separated populations to argument ref pops as shown below
<pre>
Rscript FastNGSAdmixPCA.r infile=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz refpops=YRI,JPT,CHB,CEU
</pre>

=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.

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

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>

FastNgsAdmixOld

2014-10-15T13:27:30Z

Kehanghoej:

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 OCA of NGS data. It is based on genotype likelihoods. The program is written in R.

=Installation=
<pre>
wget http://popgen.dk/albrecht/kristian/Fast_NGS_PCA_refdata/tool.zip
unzip tool.zip
OR
Use shiny: http://popgen.dk:443/kristian/admixpca_human/
</pre>

=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
<pre>
Rscript FastNGSAdmixPCA.r infile=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz
</pre>
All arguments can be altered. To alter the reference populations one need to write comma separated populations to argument ref pops as shown below
<pre>
YRI,JPT,CHB,CEU
</pre>

=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.

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

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>

FastNgsAdmixOld

2014-10-15T13:27:08Z

Kehanghoej:

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 OCA of NGS data. It is based on genotype likelihoods. The program is written in R.

=Installation=
<pre>
wget http://popgen.dk/albrecht/kristian/Fast_NGS_PCA_refdata/tool.zip
unzip tool.zip
OR
Use shiny: http://popgen.dk:443/kristian/admixpca_human/
</pre>

=Run example=
tool.zip contains all files 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
<pre>
Rscript FastNGSAdmixPCA.r infile=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz
</pre>
All arguments can be altered. To alter the reference populations one need to write comma separated populations to argument ref pops as shown below
<pre>
YRI,JPT,CHB,CEU
</pre>

=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.

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

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>

FastNgsAdmixOld

2014-10-15T13:26:19Z

Kehanghoej:

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=
<pre>
wget http://popgen.dk/albrecht/kristian/Fast_NGS_PCA_refdata/tool.zip
unzip tool.zip
OR
Use shiny: http://popgen.dk:443/kristian/admixpca_human/
</pre>

=Run example=
tool.zip contains all files 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
<pre>
Rscript FastNGSAdmixPCA.r infile=NA12763.mapped.ILLUMINA.bwa.CEU.low_coverage.20130502.bam.beagle.gz
</pre>
All arguments can be altered. To alter the reference populations one need to write comma separated populations to argument ref pops as shown below
<pre>
YRI,JPT,CHB,CEU
</pre>

=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.

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

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>

FastNgsAdmixOld

2014-10-15T13:18:33Z

Kehanghoej:

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=
<pre>
wget http://popgen.dk/albrecht/kristian/Fast_NGS_PCA_refdata/tool.zip
unzip tool.zip
OR
Use shiny: http://popgen.dk:443/kristian/admixpca_human/
</pre>

=Run example=
tool.zip contains all files 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/
<pre>
wget popgen.dk/??????/popfreq.RData
wget popgen.dk/??????/beagle.gz
</pre>
tralalala
<pre>
YRI, CEU, Sardinian, WestGreenland, CHB, JPT, Sindhi, Papuan, Chukchi, Karitiana
</pre>

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

<pre>
HOME$ Rscript NGS_Admix_rscript.r beagle_GL='indi_genotypelikelihood.beagle' popfreq_RDATA='pop_freq_all.RData' outputfile='test'
</pre>

=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.

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

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>

FastNgsAdmixOld

2014-09-21T20:44:05Z

Kehanghoej:

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=
<pre>
wget popgen.dk/??
OR
Use shiny: popgen.dk/???
</pre>

=Run example=
First download some example test files which has been generated on basis of data from the 1000 genomes project.
<pre>
wget popgen.dk/??????/popfreq.RData
wget popgen.dk/??????/beagle.gz
</pre>
tralalala
<pre>
YRI, CEU, Sardinian, WestGreenland, CHB, JPT, Sindhi, Papuan, Chukchi, Karitiana
</pre>

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

<pre>
HOME$ Rscript NGS_Admix_rscript.r beagle_GL='indi_genotypelikelihood.beagle' popfreq_RDATA='pop_freq_all.RData' outputfile='test'
</pre>

=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.

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

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>

FastNgsAdmixOld

2014-09-21T20:41:44Z

Kehanghoej:

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=
<pre>
wget popgen.dk/??
OR
Use shiny: popgen.dk/???
</pre>

=Run example=
First download some example test files which has been generated on basis of data from the 1000 genomes project.
<pre>
wget popgen.dk/??????/popfreq.RData
wget popgen.dk/??????/beagle.gz
</pre>
tralalala
<pre>
YRI, CEU, Sardinian, WestGreenland, CHB, JPT, Sindhi, Papuan, Chukchi, Karitiana
</pre>

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

<pre>
HOME$ Rscript NGS_Admix_rscript.r beagle_GL='indi_genotypelikelihood.beagle' popfreq_RDATA='pop_freq_all.RData' outputfile='test'
</pre>

=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.

The example below show how to make a beagle file of genotype likelihood using ANGSD.
<pre>
HOME$ /home/software/angsd/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
</pre>

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>

FastNgsAdmixOld

2014-09-21T20:15:32Z

Kehanghoej:

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=
<pre>
wget popgen.dk/??
OR
Use shiny: popgen.dk/???
</pre>

=Run example=
First download some example test files which has been generated on basis of data from the 1000 genomes project.
<pre>
wget popgen.dk/??????/popfreq.RData
wget popgen.dk/??????/beagle.gz
</pre>
tralalala
<pre>
YRI, CEU, Sardinian, WestGreenland, CHB, JPT, Sindhi, Papuan, Chukchi, Karitiana
</pre>

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

<pre>
HOME$ Rscript NGS_Admix_rscript.r beagle_GL='indi_genotypelikelihood.beagle' popfreq_RDATA='pop_freq_all.RData' outputfile='test'
</pre>

=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>

FastNgsAdmixOld

2014-09-21T20:13:34Z

Kehanghoej:

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=
<pre>
wget popgen.dk/??
OR
Use shiny: popgen.dk/???
</pre>

=Run example=
First download some example test files which has been generated on basis of data from the 1000 genomes project.
<pre>
wget popgen.dk/??????/popfreq.RData
wget popgen.dk/??????/beagle.gz
</pre>
tralalala
<pre>
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'
</pre>

=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>

FastNgsAdmixOld

2014-09-21T20:13:05Z

Kehanghoej:

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=
<pre>
wget popgen.dk/??
OR
Use shiny: popgen.dk/???
</pre>

=Run example=
First download some example test files which has been generated on basis of data from the 1000 genomes project.
<pre>
wget popgen.dk/??????/popfreq.RData
wget popgen.dk/??????/beagle.gz
</pre>
tralalala
<pre>
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'
</pre>

=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>

FastNgsAdmixOld

2014-09-21T20:12:41Z

Kehanghoej:

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=
<pre>
wget popgen.dk/??
OR
Use shiny: popgen.dk/???
</pre>

=Run example=
First download some example test files which has been generated on basis of data from the 1000 genomes project.
<pre>
wget popgen.dk/??????/popfreq.RData
wget popgen.dk/??????/beagle.gz
</pre>

<pre>
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'
</pre>

=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>

FastNgsAdmixOld

2014-09-21T20:11:32Z

Kehanghoej:

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=
<pre>
wget popgen.dk/??
OR
Use shiny: popgen.dk/???
</pre>

=Run example=
First download some example test files which has been generated on basis of data from the 1000 genomes project.
<pre>
wget popgen.dk/??????/popfreq.RData
wget popgen.dk/??????/beagle.gz
</pre>

<pre>
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'
</pre>

=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>

FastNgsAdmixOld

2014-09-21T20:11:15Z

Kehanghoej:

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=
<pre>
wget popgen.dk/??
OR
Use shiny: popgen.dk/???
</pre>

=Run example=
First download some example test files which has been generated on basis of data from the 1000 genomes project.
<pre>
wget popgen.dk/??????/popfreq.RData
wget popgen.dk/??????/beagle.gz
</pre>

<pre>
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'
</pre>

=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>

FastNgsAdmixOld

2014-09-21T19:59:48Z

Kehanghoej:

FastNgsAdmixOld

2014-09-21T19:59:13Z

Kehanghoej:

FastNgsAdmixOld

2014-09-21T19:18:31Z

Kehanghoej:

FastNgsAdmixOld

2014-09-21T19:18:06Z

Kehanghoej:

FastNgsAdmixOld

2014-09-21T19:17:49Z

Kehanghoej:

FastNgsAdmixOld

2014-09-21T19:11:31Z

Kehanghoej:

FastNgsAdmixOld

2014-09-21T18:59:58Z

Kehanghoej:

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=
adfadsfasdfasdfasdfdasfasdfdasfasd
fasdfadsfadsf
adsfasdfasdf
dasfasdfasd

=Run example=

=Input Files=

FastNgsAdmixOld

2014-09-21T18:58:24Z

Kehanghoej:

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=
adfadsfasdfasdfasdfdasfasdfdasfasd
fasdfadsfadsf
adsfasdfasdf
dasfasdfasd

=Run_example=

=Input_Files=

FastNgsAdmixOld

2014-09-21T18:57:51Z

Kehanghoej:

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=
adfadsfasdfasdfasdfdasfasdfdasfasd
fasdfadsfadsf
adsfasdfasdf
dasfasdfasd

=Run_example=

FastNgsAdmixOld

2014-09-21T18:57:22Z

Kehanghoej:

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=
adfadsfasdfasdfasdfdasfasdfdasfasd
fasdfadsfadsf
adsfasdfasdf
dasfasdfasd

FastNgsAdmixOld

2014-09-21T18:56:16Z

Kehanghoej:

FastNgsAdmixOld

2014-09-21T18:48:55Z

Kehanghoej:

FastNgsAdmixOld

2014-09-21T18:46:29Z

Kehanghoej:

FastNgsAdmixOld

2014-09-21T18:45:04Z

Kehanghoej: Created page with "This page contains information about the program called NGSadmix, which is a very nice tool for finding admixture proportions from NGS data. It is based on genotype likelihood..."

This page contains information about the program called NGSadmix, which is a very nice tool for finding admixture proportions from NGS data. It is based on genotype likelihoods. It is a fancy multithreaded c/c++ program. We really like it.