Admixture with Reference

Data preparation

In our analysis we are using the 5-meta populations from Shriner et al. (PMID: 37653728) which is in the folder "Parentals" in this GitHub. We are assuming that the data are formatted as PFILES (Plink2 format). You can generate the list of variants in common, remove the LD and generate the .pop file you can use the prepareAdmixture.py. In order to generate: list of variants in common, remove the LD, and generate the .pop file, use the prepareAdmixture.py.

Example of command line

python3.8 prepareAdmixture.py \
-i /my/folder/with/QCed/Data/LARGE_Phase2_HWECase \
-I /my/folder/with/my/1000G/Reference/Extracted/OneThousand_All \
-o ./Admixture -F ./Parentals -P /home/peixott/beegfs/Programs/plink2 -p plink -c \
admixture --cv LD_Bfile1And2.bed 5 -j40 --supervised | tee log5_1.out

Parameters

Merge PFiles to Admixture

options:
  -h, --help            show this help message and exit

Required arguments for all steps:
  -i INPUT1, --input1 INPUT1
                        First pfile. We recommend this file be with the lower number of variants
  -I INPUT2, --input2 INPUT2
                        Second pfile.
  -o OUTPUT, --output OUTPUT
                        Name of output folder
  -F PARENTALSFOLDER, --parentalsFolder PARENTALSFOLDER
                        Folder with files with parentals ID
  -P PLINK2, --plink2 PLINK2
                        Plink2 executable
  -p PLINK, --plink PLINK
                        Plink executable

Optional arguments:
  -c, --covar           Remove NA covar

Acknowledgements

This work is supported by NIH Grant R01 1R01NS112499-01A1, MJFF Grant ID: 18298, ASAP-GP2 and Parkinson's Foundation

Contact

Created by Thiago Peixoto Leal. PhD (PEIXOTT@ccf.org or thpeixotol@hotmail.com)