Inferring ancestry using the 1000 Genomes high coverage reference and admixture (https://dalexander.github.io/admixture/)
wget https://dalexander.github.io/admixture/binaries/admixture_linux-1.3.0.tar.gz
tar -xvf admixture_linux-1.3.0.tar.gz
export PATH="$HOME/admixture/dist/admixture_linux-1.3.0:$PATH"
| Code | Population Name | Superpopulation |
|---|---|---|
| AFR_ACB | African Caribbeans in Barbados | AFR (African) |
| AFR_ASW | African Ancestry in Southwest US | AFR (African) |
| AFR_ESN | Esan in Nigeria | AFR (African) |
| AFR_GWD | Gambian in Western Divisions | AFR (African) |
| AFR_LWK | Luhya in Webuye | AFR (African) |
| AFR_MSL | Mende in Sierra Leone | AFR (African) |
| AFR_YRI | Yoruba in Ibadan | AFR (African) |
| AMR_CLM | Colombians in Medellín | AMR (Admixed American) |
| AMR_MXL | Mexican Ancestry in Los Angeles | AMR (Admixed American) |
| AMR_PEL | Peruvians in Lima | AMR (Admixed American) |
| AMR_PUR | Puerto Ricans in Puerto Rico | AMR (Admixed American) |
| EAS_CDX | Chinese Dai in Xishuangbanna | EAS (East Asian) |
| EAS_CHB | Han Chinese in Beijing | EAS (East Asian) |
| EAS_CHS | Southern Han Chinese | EAS (East Asian) |
| EAS_JPT | Japanese in Tokyo | EAS (East Asian) |
| EAS_KHV | Kinh in Ho Chi Minh City | EAS (East Asian) |
| EUR_CEU | Utah Residents (CEPH) with NW European ancestry | EUR (European) |
| EUR_FIN | Finnish in Finland | EUR (European) |
| EUR_GBR | British in England and Scotland | EUR (European) |
| EUR_IBS | Iberian Population in Spain | EUR (European) |
| EUR_TSI | Toscani in Italy | EUR (European) |
| SAS_BEB | Bengali in Bangladesh | SAS (South Asian) |
| SAS_GIH | Gujarati Indian in Houston | SAS (South Asian) |
| SAS_ITU | Indian Telugu in the UK | SAS (South Asian) |
| SAS_PJL | Punjabi in Lahore | SAS (South Asian) |
| SAS_STU | Sri Lankan Tamil in the UK | SAS (South Asian) |
Prerequsities are a reference file, e.g. the high coverage 1KG reference file 1KG_high_coverage_20130606_g1k_3202.merged containing 26 subpopulations and 5 superpopulations.
Your reference file should contain information about the ancestry of individuals e.g. in the FID, which is needed to create the .pop file for supervised ADMIXTURE ancestry inference.
For more details check out the ADMIXTURE manual.
Ideally, files are RICOPILI were QCed using the (RICOPILI)[https://github.com/Ripkelab/ricopili] preimp_dir and pcaer modules.
# replace PLINK prefix and output filename
sbatch 1_run_admixture.sh your_bfile your_outname