Example files from BPGA paper

Genotype data from HapMap Phase 3 were downloaded from the public repository (ftp: https://ftp.ncbi.nlm.nih.gov/hapmap/genotypes/hapmap3/plink_format/draft_1/; file hapmap3_r1_b36_fwd.qc.poly.tar.bz2). The archive was decompressed, and PED/MAP files were converted to binary BED/BIM/FAM and filtered to MAF ≥ 0.05 with PLINK. A random set of 10,000 autosomal SNPs were extracted and used to filter full data set to obtain a final hapmap3_r1_b36 10K sample to test BPGA functionality. Fam file was formatted according BPGA data model as “pop1pop2” were POP1 were superpopulations (AFR=African; AMR=Admixed American; EAS=East Asian; EUR=European; SAS=South Asian) and POP2 subpopulations (ASW [African ancestry in Southwest USA], CEU [Utah residents with Northern and Western European ancestry from the CEPH collection], CHB [Han Chinese in Beijing, China], CHD [Chinese in Metropolitan Denver, Colorado], GIH [Gujarati Indians in Houston, Texas], JPT [Japanese in Tokyo, Japan], LWK [Luhya in Webuye, Kenya], MEX [Mexican ancestry in Los Angeles, California], MKK [Maasai in Kinyawa, Kenya], TSI [Toscans in Italy], YRI [Yoruba in Ibadan, Nigeria]). Geographic coordinates were assigned according to each population’s geographic origin.