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tum2pop-mapping

Population origin mapping from cancer SNP profile into 5 continental groups as defined in 1000 Genomes Project. This tool supports mapping from B-allele frequency data generated with 9 Affymetrix SNP array platforms as input and a population assignment to one of the five continental groups -- AFR(Africa), EUR (Europe), AMR(South America), EAS (East Asia), SAS (South Asia). The currently supported genome version is GRCh37 (hg19). A mapping to other genome versions is planned.

Docker version installation

The easiest way is to use docker application. First, install Docker application, then:

docker pull qingyao/tum2pop

Usage

First, you would like to create a working directory $hostdir (use absolute path) to place your input files and to receive the output from the pipeline.

docker run -it --rm --mount type=bind,source=$hostdir,target=/data qingyao/tum2pop

After entering the interactive mode of the container, you can place your input files in $hostdir/input directory. Then:

Rscript --vanilla run_pop.r <parameters>

Then you will receive in the /results folder under $hostdir your mapping results.

Example

You need to download the /test folder here and copy the absolute path as $test_dir.

docker run -it --rm --mount type=bind,source=$test_dir,target=/data qingyao/tum2pop

Rscript --vanilla run_pop.r -i BAF -o CONT -p Mapping250K_Nsp

Options

-i --input TEXT input as B allele frequency file format (BAF), or genotype calling format (GC), or Birdseed genotype format (BS).

-p --platform TEXT SNP array platform

-o --output TEXT output as 6 theoretical fractions (FRAC), or standard output as ratio of 5 continents and a voting result (CONT)

The current pipeline supports 9 SNP array platforms from Affymetrix:

  • Mapping10K_Xba142

  • Mapping50K_Hind240

  • Mapping50K_Xba240

  • Mapping250K_Nsp

  • Mapping250K_Sty

  • GenomeWideSNP_5

  • GenomeWideSNP_6

  • CytoScan750K_Array

  • CytoScanHD_Array

The input file should be tab separated. There should be 4 columns: ID (SNP ID or simply indicating row number), chromosome (1-23), nucleotide base position, and a value column (a number within 0-1 if BAF format, or AA/AB/BB if GC format).

Example for BAF input format:

ID CHRO BASEPOS VALUE

SNP_A-2131660 1 1220751 0.3487

SNP_A-1967418 1 2302812 0.9451

SNP_A-1969580 1 2398125 1.0000

SNP_A-4263484 1 2622185 0.4612

.

.

.

Example for GC input format:

ID CHRO BASEPOS VALUE

SNP_1 1 1220751 AB

SNP_2 1 2302812 BB

SNP_3 1 2398125 BB

SNP_4 1 2622185 AB

.

.

.

Example for BS input format:

ID CHRO BASEPOS VALUE

SNP_1 1 1220751 1

SNP_2 1 2302812 2

SNP_3 1 2398125 2

SNP_4 1 2622185 1

.

.

.