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.
The easiest way is to use docker application. First, install Docker application, then:
docker pull qingyao/tum2pop
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.
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
-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
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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
.
.
.